5HJY | pdb_00005hjy

Structure function studies of R. palustris RubisCO (I165T mutant; CABP-bound)

PDB DOI: https://doi.org/10.2210/pdb5HJY/pdb

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

Deposited: 2016-01-13 Released: 2017-01-18
Deposition Author(s): Arbing, M.A., Shin, A., Cascio, D., Satagopan, S., North, J.A., 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 ?
R-Value Free:
0.225 (Depositor), 0.230 (DCC)
R-Value Work:
0.183 (Depositor), 0.190 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Structure function studies of R. palustris RubisCO.

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

To be published.

Macromolecule Content

Total Structure Weight: 318.79 kDa
Atom Count: 22,581
Modelled Residue Count: 2,729
Deposited Residue Count: 2,886
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	481	Rhodopseudomonas palustris	Mutation(s): 1 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 G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth C] SDF format, chain M [auth D] SDF format, chain P [auth E] SDF format, chain R [auth F] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth D] MOL2 format, chain P [auth E] MOL2 format, chain R [auth F] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth D] mmCIF format, chain P [auth E] mmCIF format, chain R [auth F]	G [auth A] I [auth B] K [auth C] M [auth D] P [auth E] G [auth A], I [auth B], K [auth C], M [auth D], P [auth E], R [auth F]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C₆ H₁₄ O₁₃ P₂ ITHCSGCUQDMYAI-ZMIZWQJLSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain P [auth E] Focus chain R [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain N [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain N [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain L [auth C] mmCIF format, chain N [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F]	H [auth A] J [auth B] L [auth C] N [auth D] Q [auth E] H [auth A], J [auth B], L [auth C], N [auth D], Q [auth E], S [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain Q [auth E] Focus chain S [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	L-PEPTIDE LINKING	C₇ H₁₄ N₂ O₄		LYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 ?
R-Value Free: 0.225 (Depositor), 0.230 (DCC)
R-Value Work: 0.183 (Depositor), 0.190 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 73.86	α = 107.84
b = 100.02	β = 113.77
c = 103.56	γ = 96.09

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2017-01-18

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: 2017-01-18
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: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-15
Changes: Data collection

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Structure function studies of R. palustris RubisCO (I165T mutant; CABP-bound)

Structure function studies of R. palustris RubisCO.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations