7ZX3 | pdb_00007zx3

C295D Mutant of Recombinant CODH-II

PDB DOI: https://doi.org/10.2210/pdb7ZX3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Carboxydothermus hydrogenoformans Z-2901
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-05-20 Released: 2023-03-15
Deposition Author(s): Basak, Y., Jeoung, J.H., Dobbek, H.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free:
0.185 (Depositor), 0.152 (DCC)
R-Value Work:
0.150 (Depositor), 0.151 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7ZX3

This is version 1.1 of the entry. See complete history.

Literature

Substrate Activation at the Ni,Fe Cluster of CO Dehydrogenases: The Influence of the Protein Matrix

Basak, Y., Jeoung, J.H., Domnik, L., Ruickoldt, J., Dobbek, H.

(2022) ACS Catal

DOI: https://doi.org/10.1021/acscatal.2c02922

Macromolecule Content

Total Structure Weight: 68.22 kDa
Atom Count: 5,264
Modeled Residue Count: 633
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase 2	A [auth X]	636	Carboxydothermus hydrogenoformans Z-2901	Mutation(s): 1 Gene Names: cooS2, cooSII, CHY_0085 EC: 1.2.7.4
UniProt
Find proteins for Q9F8A8 (Carboxydothermus hydrogenoformans (strain ATCC BAA-161 / DSM 6008 / Z-2901)) Explore Q9F8A8 Go to UniProtKB: Q9F8A8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9F8A8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain B [auth X] SDF format, chain D [auth X] MOL2 format, chain B [auth X] MOL2 format, chain D [auth X] mmCIF format, chain B [auth X] mmCIF format, chain D [auth X]	B [auth X], D [auth X]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain B [auth X] Focus chain D [auth X] Interactions & Density Focus chain B [auth X] Focus chain D [auth X]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth X] SDF format, chain G [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X]	F [auth X], G [auth X]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain F [auth X] Focus chain G [auth X] Interactions & Density Focus chain F [auth X] Focus chain G [auth X]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth X] MOL2 format, chain E [auth X] mmCIF format, chain E [auth X]	E [auth X]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth X] Interactions & Density Focus chain E [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.68 Å
R-Value Free: 0.185 (Depositor), 0.152 (DCC)
R-Value Work: 0.150 (Depositor), 0.151 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.87	α = 90
b = 75.05	β = 111.66
c = 71.73	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-15

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG DO 785/6-2

Revision History (Full details and data files)

Version 1.0: 2023-03-15
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, 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.