2X1Z

Structure of Peridinin-Chlorophyll-Protein reconstituted with Chl-d

PDB DOI: https://doi.org/10.2210/pdb2X1Z/pdb

Classification: PHOTOSYNTHESIS
Organism(s): Amphidinium carterae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-01-09 Released: 2010-02-09
Deposition Author(s): Schulte, T., Hiller, R.G., Hofmann, E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.183
R-Value Work: 0.141
R-Value Observed: 0.143

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

X-Ray Structures of the Peridinin-Chlorophyll-Protein Reconstituted with Different Chlorophylls.

Schulte, T., Hiller, R.G., Hofmann, E.

(2010) FEBS Lett 584: 973

PubMed: 20102711 Search on PubMed
DOI: https://doi.org/10.1016/j.febslet.2010.01.041
Primary Citation of Related Structures:
2X1Z, 2X20, 2X21

PubMed Abstract:
The peridinin-chlorophyll a-protein (PCP) from dinoflagellates is a soluble light harvesting antenna which gathers incoming photons mainly by the carotenoid peridinin. In PCPs reconstituted with different chlorophylls, the peridinin to chlorophyll energy transfer rates are well predicted by a F?rster-like theory, but only if the pigment arrangements are identical in all PCPs. We have determined the X-ray structures of PCPs reconstituted with Chlorophyll-b (Chl-b), Chlorophyll-d (Chl-d) and Bacteriochlorophyll-a (BChl-a) to resolutions

Organizational Affiliation

Biophysics, Department of Biology and Biotechnology, Ruhr-University Bochum, D-44780 Bochum, Germany.

Macromolecule Content

Total Structure Weight: 21.29 kDa
Atom Count: 1,758
Modelled Residue Count: 151
Deposited Residue Count: 151
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PERIDININ-CHLOROPHYLL A-BINDING PROTEIN, CHLOROPLASTIC	A [auth M]	151	Amphidinium carterae	Mutation(s): 0
UniProt
Find proteins for P80484 (Amphidinium carterae) Explore P80484 Go to UniProtKB: P80484
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P80484
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD Query on DGD Download Ideal Coordinates CCD File SDF format, chain G [auth M] MOL2 format, chain G [auth M] mmCIF format, chain G [auth M]	G [auth M]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain G [auth M] Interactions & Density Focus chain G [auth M]
CL7 Query on CL7 Download Ideal Coordinates CCD File SDF format, chain F [auth M] MOL2 format, chain F [auth M] mmCIF format, chain F [auth M]	F [auth M]	CHLOROPHYLL D C₅₄ H₇₀ Mg N₄ O₆ FBCRYORFRGRJBC-ACDPFEIMSA-L		Interactions Focus chain F [auth M] Interactions & Density Focus chain F [auth M]
PID Query on PID Download Ideal Coordinates CCD File SDF format, chain B [auth M] SDF format, chain C [auth M] SDF format, chain D [auth M] SDF format, chain E [auth M] MOL2 format, chain B [auth M] MOL2 format, chain C [auth M] MOL2 format, chain D [auth M] MOL2 format, chain E [auth M] mmCIF format, chain B [auth M] mmCIF format, chain C [auth M] mmCIF format, chain D [auth M] mmCIF format, chain E [auth M]	B [auth M], C [auth M], D [auth M], E [auth M]	PERIDININ C₃₉ H₅₀ O₇ UYRDHEJRPVSJFM-FROCQLDGSA-N		Interactions Focus chain B [auth M] Focus chain C [auth M] Focus chain D [auth M] Focus chain E [auth M] Interactions & Density Focus chain B [auth M] Focus chain C [auth M] Focus chain D [auth M] Focus chain E [auth M]
CD Query on CD Download Ideal Coordinates CCD File SDF format, chain O [auth M] SDF format, chain P [auth M] SDF format, chain Q [auth M] SDF format, chain R [auth M] SDF format, chain S [auth M] SDF format, chain T [auth M] MOL2 format, chain O [auth M] MOL2 format, chain P [auth M] MOL2 format, chain Q [auth M] MOL2 format, chain R [auth M] MOL2 format, chain S [auth M] MOL2 format, chain T [auth M] mmCIF format, chain O [auth M] mmCIF format, chain P [auth M] mmCIF format, chain Q [auth M] mmCIF format, chain R [auth M] mmCIF format, chain S [auth M] mmCIF format, chain T [auth M]	O [auth M] P [auth M] Q [auth M] R [auth M] S [auth M] O [auth M], P [auth M], Q [auth M], R [auth M], S [auth M], T [auth M]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M] Interactions & Density Focus chain O [auth M] Focus chain P [auth M] Focus chain Q [auth M] Focus chain R [auth M] Focus chain S [auth M] Focus chain T [auth M]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain L [auth M] MOL2 format, chain L [auth M] mmCIF format, chain L [auth M]	L [auth M]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain L [auth M] Interactions & Density Focus chain L [auth M]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain H [auth M] SDF format, chain M SDF format, chain N [auth M] SDF format, chain I [auth M] MOL2 format, chain H [auth M] MOL2 format, chain M MOL2 format, chain N [auth M] MOL2 format, chain I [auth M] mmCIF format, chain H [auth M] mmCIF format, chain M mmCIF format, chain N [auth M] mmCIF format, chain I [auth M]	H [auth M], I [auth M], M, N [auth M]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth M] Focus chain I [auth M] Focus chain M Focus chain N [auth M] Interactions & Density Focus chain H [auth M] Focus chain I [auth M] Focus chain M Focus chain N [auth M]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain J [auth M] SDF format, chain K [auth M] MOL2 format, chain J [auth M] MOL2 format, chain K [auth M] mmCIF format, chain J [auth M] mmCIF format, chain K [auth M]	J [auth M], K [auth M]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth M] Focus chain K [auth M] Interactions & Density Focus chain J [auth M] Focus chain K [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 ?
R-Value Free: 0.183
R-Value Work: 0.141
R-Value Observed: 0.143
Space Group: C 2 2 2₁

Unit Cell:

Length ( ? )	Angle ( ? )
a = 68.58	α = 90
b = 81.99	β = 90
c = 75.24	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-02-09

Deposition Author(s):

Schulte, T.

Hiller, R.G.

Hofmann, E.

Revision History (Full details and data files)

Version 1.0: 2010-02-09
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-01-30
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2019-02-06
Changes: Data collection, Experimental preparation
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description