6NW0 | pdb_00006nw0

Crystal Structure Desulfovibrio desulfuricans Nickel-Substituted Rubredoxin

• PDB DOI: https://doi.org/10.2210/pdb6NW0/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Desulfovibrio desulfuricans
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2019-02-05 Released: 2019-08-14 
• Deposition Author(s): Slater, J.W., Marguet, S.C., Gray, M.E., Sotomayor, M., Shafaat, H.S.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

The Power of the Secondary Sphere: Modulating Hydrogenase Activity in Nickel-Substituted Rubredoxin

Slater, J.W., Marguet, S.C., Gray, M.E., Monaco, H.A., Sotomayor, M., Shafaat, H.S.

(2019) ACS Catal 

• DOI: https://doi.org/10.1021/acscatal.9b01720

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 10.35 kDa 
• Atom Count: 796 
• Modeled Residue Count: 90 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A, B	45	Desulfovibrio desulfuricans	Mutation(s): 0  Gene Names: SAMN02910291_00071, rd1
UniProt
Find proteins for P04170 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore P04170  Go to UniProtKB:  P04170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NI	C [auth A], D [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.29	α = 90
b = 51.436	β = 128
c = 39.697	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-14 
Deposition Author(s): Slater, J.W., Marguet, S.C., Gray, M.E., Sotomayor, M., Shafaat, H.S.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	CHE-1454289

Revision History  

• Version 1.0: 2019-08-14
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description