3WQP | pdb_00003wqp

Crystal structure of Rubisco T289D mutant from Thermococcus kodakarensis

PDB DOI: https://doi.org/10.2210/pdb3WQP/pdb

Classification: LYASE
Organism(s): Thermococcus kodakarensis KOD1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2014-01-29 Released: 2015-02-04
Deposition Author(s): Fujihashi, M., Nishitani, Y., Kiriyama, T., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.25 ?
R-Value Free:
0.258 (Depositor), 0.250 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Mutation design of thermophilic Rubisco based on the three-dimensional structure enhances its activity at ambient temperature

Kiriyama, T., Fujihashi, M., Nishitani, Y., Aono, R., Sato, T., Takai, T., Tagashira, K., Fukuda, W., Atomi, H., Imanaka, T., Miki, K.

To be published.

Macromolecule Content

Total Structure Weight: 502.76 kDa
Atom Count: 36,577
Modeled Residue Count: 4,369
Deposited Residue Count: 4,440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	444	Thermococcus kodakarensis KOD1	Mutation(s): 1 Gene Names: rbcL, rbc, TK2290 EC: 4.1.1.39
UniProt
Find proteins for O93627 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore O93627 Go to UniProtKB: O93627
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O93627
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAP Query on CAP Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain CA [auth G] SDF format, chain EA [auth H] SDF format, chain IA [auth I] SDF format, chain L [auth A] SDF format, chain MA [auth J] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain EA [auth H] MOL2 format, chain IA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain EA [auth H] mmCIF format, chain IA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	AA [auth F] CA [auth G] EA [auth H] IA [auth I] L [auth A] AA [auth F], CA [auth G], EA [auth H], IA [auth I], L [auth A], MA [auth J], O [auth B], R [auth C], U [auth D], X [auth E]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain IA [auth I] Focus chain L [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain IA [auth I] Focus chain L [auth A] Focus chain MA [auth J] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain GA [auth H] SDF format, chain JA [auth I] SDF format, chain KA [auth I] SDF format, chain M [auth A] SDF format, chain NA [auth J] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain JA [auth I] MOL2 format, chain KA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain JA [auth I] mmCIF format, chain KA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth E]	FA [auth H] GA [auth H] JA [auth I] KA [auth I] M [auth A] FA [auth H], GA [auth H], JA [auth I], KA [auth I], M [auth A], NA [auth J], P [auth B], S [auth C], V [auth D], Y [auth E]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain FA [auth H] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain FA [auth H] Focus chain GA [auth H] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain BA [auth G] SDF format, chain DA [auth H] SDF format, chain HA [auth I] SDF format, chain K [auth A] SDF format, chain LA [auth J] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] SDF format, chain W [auth E] SDF format, chain Z [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain K [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F]	BA [auth G] DA [auth H] HA [auth I] K [auth A] LA [auth J] BA [auth G], DA [auth H], HA [auth I], K [auth A], LA [auth J], N [auth B], Q [auth C], T [auth D], W [auth E], Z [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain HA [auth I] Focus chain K [auth A] Focus chain LA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain HA [auth I] Focus chain K [auth A] Focus chain LA [auth J] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Focus chain W [auth E] Focus chain Z [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX Query on KCX	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.25 ?
R-Value Free: 0.258 (Depositor), 0.250 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( ? )	Angle ( ? )
a = 170.566	α = 90
b = 246.238	β = 90
c = 144.628	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-02-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-02-04
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection