5KOZ

Structure function studies of R. palustris RubisCO (K192C mutant; CABP-bound)

PDB DOI: https://doi.org/10.2210/pdb5KOZ/pdb

Classification: LYASE
Organism(s): Rhodopseudomonas palustris
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-07-01 Released: 2017-07-05
Deposition Author(s): Arbing, M.A., North, J.A., Satagopan, S., Tabita, F.R.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.247
R-Value Work: 0.200
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure function studies of R. palustris RubisCO.

Arbing, M.A., North, J.A., Satagopan, S., Varaljay, V.A., Shin, A., Tabita, F.R.

To be published.

Macromolecule Content

Total Structure Weight: 637.54 kDa
Atom Count: 44,037
Modelled Residue Count: 5,464
Deposited Residue Count: 5,772
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, K, L	481	Rhodopseudomonas palustris	Mutation(s): 1 Gene Names: cbbM, RPA4641 EC: 4.1.1.39
UniProt
Find proteins for Q6N0W9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N0W9 Go to UniProtKB: Q6N0W9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6N0W9
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 BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] 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 QA [auth K] SDF format, chain S [auth C] SDF format, chain TA [auth L] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] 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 QA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain TA [auth L] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E]	BA [auth F] EA [auth G] HA [auth H] KA [auth I] M [auth A] BA [auth F], EA [auth G], HA [auth H], KA [auth I], M [auth A], NA [auth J], P [auth B], QA [auth K], S [auth C], TA [auth L], V [auth D], Y [auth E]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E]
CO3 Query on CO3 Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain DA [auth F] SDF format, chain GA [auth G] SDF format, chain JA [auth H] SDF format, chain MA [auth I] SDF format, chain O [auth A] SDF format, chain PA [auth J] SDF format, chain R [auth B] SDF format, chain SA [auth K] SDF format, chain U [auth C] SDF format, chain VA [auth L] SDF format, chain X [auth D] MOL2 format, chain AA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain GA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain MA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth K] MOL2 format, chain U [auth C] MOL2 format, chain VA [auth L] MOL2 format, chain X [auth D]	AA [auth E] DA [auth F] GA [auth G] JA [auth H] MA [auth I] AA [auth E], DA [auth F], GA [auth G], JA [auth H], MA [auth I], O [auth A], PA [auth J], R [auth B], SA [auth K], U [auth C], VA [auth L], X [auth D]	CARBONATE ION C O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-L		Interactions Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D] Interactions & Density Focus chain AA [auth E] Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain MA [auth I] Focus chain O [auth A] Focus chain PA [auth J] Focus chain R [auth B] Focus chain SA [auth K] Focus chain U [auth C] Focus chain VA [auth L] Focus chain X [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain IA [auth H] SDF format, chain LA [auth I] SDF format, chain N [auth A] SDF format, chain OA [auth J] SDF format, chain Q [auth B] SDF format, chain RA [auth K] SDF format, chain T [auth C] SDF format, chain UA [auth L] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain LA [auth I] MOL2 format, chain N [auth A] MOL2 format, chain OA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain RA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain UA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E]	CA [auth F] FA [auth G] IA [auth H] LA [auth I] N [auth A] CA [auth F], FA [auth G], IA [auth H], LA [auth I], N [auth A], OA [auth J], Q [auth B], RA [auth K], T [auth C], UA [auth L], W [auth D], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain N [auth A] Focus chain OA [auth J] Focus chain Q [auth B] Focus chain RA [auth K] Focus chain T [auth C] Focus chain UA [auth L] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain LA [auth I] Focus chain N [auth A] Focus chain OA [auth J] Focus chain Q [auth B] Focus chain RA [auth K] Focus chain T [auth C] Focus chain UA [auth L] Focus chain W [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.247
R-Value Work: 0.200
R-Value Observed: 0.205
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.46	α = 89.96
b = 110.62	β = 101.77
c = 166.85	γ = 104.88

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-07-05

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM095742
Department of Energy (DOE, United States)	United States	DE-FC02-02ER63421

Revision History (Full details and data files)

Version 1.0: 2017-07-05
Type: Initial release
Version 1.1: 2017-09-27
Changes: Author supporting evidence
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description