6NW1 | pdb_00006nw1

Crystal Structure Desulfovibrio desulfuricans Nickel-Substituted Rubredoxin V37N

PDB DOI: https://doi.org/10.2210/pdb6NW1/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Desulfovibrio desulfuricans
Expression System: Escherichia coli BL21
Mutation(s): Yes

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.188 (Depositor), 0.195 (DCC)
R-Value Work:
0.123 (Depositor), 0.135 (DCC)
R-Value Observed:
0.126 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

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

Macromolecule Content

Total Structure Weight: 10.38 kDa
Atom Count: 839
Modeled Residue Count: 90
Deposited Residue Count: 90
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rubredoxin	A, B	45	Desulfovibrio desulfuricans	Mutation(s): 1 Gene Names: SAMN02910291_00071, rd1
UniProt
Find proteins for P04170 (Desulfovibrio desulfuricans (strain ATCC 27774 / DSM 6949 / MB)) Explore P04170 Go to UniProtKB: P04170
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04170
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.188 (Depositor), 0.195 (DCC)
R-Value Work: 0.123 (Depositor), 0.135 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 23.718	α = 111.5
b = 25.401	β = 94.43
c = 29.084	γ = 97.52

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-14

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.