3PCQ

Femtosecond X-ray protein Nanocrystallography


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.98 ?
  • R-Value Free: 0.232 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.251 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Femtosecond X-ray protein nanocrystallography.

Chapman, H.N.Fromme, P.Barty, A.White, T.A.Kirian, R.A.Aquila, A.Hunter, M.S.Schulz, J.Deponte, D.P.Weierstall, U.Doak, R.B.Maia, F.R.Martin, A.V.Schlichting, I.Lomb, L.Coppola, N.Shoeman, R.L.Epp, S.W.Hartmann, R.Rolles, D.Rudenko, A.Foucar, L.Kimmel, N.Weidenspointner, G.Holl, P.Liang, M.Barthelmess, M.Caleman, C.Boutet, S.Bogan, M.J.Krzywinski, J.Bostedt, C.Bajt, S.Gumprecht, L.Rudek, B.Erk, B.Schmidt, C.Homke, A.Reich, C.Pietschner, D.Struder, L.Hauser, G.Gorke, H.Ullrich, J.Herrmann, S.Schaller, G.Schopper, F.Soltau, H.Kuhnel, K.U.Messerschmidt, M.Bozek, J.D.Hau-Riege, S.P.Frank, M.Hampton, C.Y.Sierra, R.G.Starodub, D.Williams, G.J.Hajdu, J.Timneanu, N.Seibert, M.M.Andreasson, J.Rocker, A.Jonsson, O.Svenda, M.Stern, S.Nass, K.Andritschke, R.Schroter, C.D.Krasniqi, F.Bott, M.Schmidt, K.E.Wang, X.Grotjohann, I.Holton, J.M.Barends, T.R.Neutze, R.Marchesini, S.Fromme, R.Schorb, S.Rupp, D.Adolph, M.Gorkhover, T.Andersson, I.Hirsemann, H.Potdevin, G.Graafsma, H.Nilsson, B.Spence, J.C.

(2011) Nature 470: 73-77

  • DOI: https://doi.org/10.1038/nature09750
  • Primary Citation of Related Structures:  
    3PCQ

  • PubMed Abstract: 

    X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (¡«200?nm to 2?¦Ìm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.


  • Organizational Affiliation

    Center for Free-Electron Laser Science, DESY, Notkestrasse 85, 22607 Hamburg, Germany. henry.chapman@desy.de


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1755Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A405 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A405
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2740Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A407 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A407
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A415 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A415
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II138Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A420 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A420
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV75Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A423 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A423
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III164Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A401 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A401
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A427 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A427
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A429 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKI [auth K]83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A425 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupP0A425
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L]154Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DGB4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DGB4
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]31Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A403 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I 4.8K proteinL [auth X]35Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKP6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
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UniProt GroupQ8DKP6
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AC [auth B]
AD [auth B]
AE [auth K]
AA [auth A],
AB [auth A],
AC [auth B],
AD [auth B],
AE [auth K],
BA [auth A],
BB [auth A],
BC [auth B],
BD [auth B],
CA [auth A],
CB [auth A],
CC [auth B],
CD [auth B],
CE [auth L],
DA [auth A],
DB [auth A],
DC [auth B],
DD [auth B],
DE [auth L],
EA [auth A],
EB [auth A],
EC [auth B],
ED [auth B],
EE [auth L],
FA [auth A],
FB [auth A],
FC [auth B],
GA [auth A],
GC [auth B],
HA [auth A],
HC [auth B],
HE [auth M],
IA [auth A],
IC [auth B],
JA [auth A],
JC [auth B],
JE [auth X],
KA [auth A],
KC [auth B],
LA [auth A],
LC [auth B],
M [auth A],
MA [auth A],
MC [auth B],
N [auth A],
NA [auth A],
NC [auth B],
O [auth A],
OA [auth A],
OC [auth B],
P [auth A],
PA [auth A],
PC [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
QC [auth B],
R [auth A],
RA [auth A],
RB [auth B],
RC [auth B],
RD [auth F],
S [auth A],
SA [auth A],
SB [auth B],
SC [auth B],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth B],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth B],
V [auth A],
VA [auth A],
VB [auth B],
VC [auth B],
VD [auth J],
W [auth A],
WA [auth A],
WB [auth B],
WC [auth B],
WD [auth J],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth B],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth B],
Z [auth A],
ZA [auth A],
ZB [auth B],
ZC [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

Download Ideal Coordinates CCD File 
ND [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
OB [auth A],
OD [auth B],
PB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
FE [auth L]
GD [auth B]
GE [auth L]
HD [auth B]
IB [auth A]
FE [auth L],
GD [auth B],
GE [auth L],
HD [auth B],
IB [auth A],
ID [auth B],
IE [auth M],
JB [auth A],
JD [auth B],
KB [auth A],
KD [auth B],
LB [auth A],
LD [auth B],
MB [auth A],
MD [auth B],
NB [auth A],
SD [auth F],
TD [auth I],
UD [auth I],
XD [auth J],
YD [auth J],
ZD [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

Download Ideal Coordinates CCD File 
FD [auth B],
GB [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
HB [auth A],
PD [auth C],
QD [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
BE [auth L]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 8.98 ?
  • R-Value Free: 0.232 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.251 
  • Space Group: P 63
Unit Cell:
Length ( ? )Angle ( ? )
a = 281¦Á = 90
b = 281¦Â = 90
c = 165.2¦Ã = 120
Software Package:
Software NamePurpose
LCLSdata collection
CASSdata collection
IDLdata collection
REFMACrefinement
CrystFELdata reduction
Montedata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2012-02-08
    Changes: Data collection
  • Version 1.3: 2012-07-25
    Changes: Non-polymer description
  • Version 1.4: 2018-01-24
    Changes: Database references
  • Version 1.5: 2018-02-14
    Changes: Data collection
  • Version 2.0: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description
  • Version 2.1: 2024-10-30
    Changes: Structure summary
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