5HAT

Structure function studies of R. palustris RubisCO (S59F/M331A mutant; CABP-bound)

• PDB DOI: https://doi.org/10.2210/pdb5HAT/pdb

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


• Deposited: 2015-12-30 Released: 2017-01-04 
• Deposition Author(s): Arbing, M.A., Leong, J.G., Cascio, D., Varaljay, V.A., 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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 

Starting Model: experimental

Literature

Structure function studies of R. palustris RubisCO.

Arbing, M.A., Satagopan, S., Varaljay, V.A., Leong, J.G., Tabita, F.R.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 637.65 kDa 
• Atom Count: 45,031 
• Modelled Residue Count: 5,467 
• Deposited Residue Count: 5,772 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribulose bisphosphate carboxylase	A, B, C, D, E, F, G, H, I, J, K, L	481	Rhodopseudomonas palustris	Mutation(s): 2  EC: 4.1.1.39
UniProt
Find proteins for Q6N0W9 (Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009)) Explore Q6N0W9  Go to UniProtKB:  Q6N0W9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CAP	AA [auth H], CA [auth I], EA [auth J], GA [auth K], IA [auth L], M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Y [auth G]	2-CARBOXYARABINITOL-1,5-DIPHOSPHATE C6 H14 O13 P2 ITHCSGCUQDMYAI-ZMIZWQJLSA-N
MG	BA [auth H], DA [auth I], FA [auth J], HA [auth K], JA [auth L], N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F], Z [auth G]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.249 
• R-Value Work: 0.213 
• R-Value Observed: 0.216 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.14	α = 90.03
b = 111.03	β = 101.69
c = 167.26	γ = 105.05

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-01-04 
Deposition Author(s): Arbing, M.A., Leong, J.G., Cascio, D., Varaljay, V.A., Satagopan, S., North, J.A., Tabita, F.R.

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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  

• Version 1.0: 2017-01-04
  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