6X5K | pdb_00006x5k

Crystal structure of CODH/ACS with carbon monoxide bound to the A-cluster

PDB DOI: https://doi.org/10.2210/pdb6X5K/pdb

Classification: OXIDOREDUCTASE/TRANSFERASE
Organism(s): Neomoorella thermoacetica
Mutation(s): No

Deposited: 2020-05-26 Released: 2020-10-07
Deposition Author(s): Cohen, S.E., Wittenborn, E.C., Hendrickson, R., Drennan, C.L.
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: 2.47 Å
R-Value Free:
0.234 (Depositor), 0.234 (DCC)
R-Value Work:
0.203 (Depositor), 0.204 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystallographic Characterization of the Carbonylated A-Cluster in Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase

Cohen, S.E., Can, M., Wittenborn, E.C., Hendrickson, R.A., Ragsdale, S.W., Drennan, C.L.

(2020) ACS Catal 10: 9741-9746

DOI: https://doi.org/10.1021/acscatal.0c03033

Macromolecule Content

Total Structure Weight: 625.36 kDa
Atom Count: 43,994
Modeled Residue Count: 5,598
Deposited Residue Count: 5,612
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit beta	A, B, C, D	674	Neomoorella thermoacetica	Mutation(s): 0 EC: 1.2.7.4
UniProt
Find proteins for P27989 (Neomoorella thermoacetica) Explore P27989 Go to UniProtKB: P27989
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27989
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon monoxide dehydrogenase/acetyl-CoA synthase subunit alpha	E [auth M], F [auth N], G [auth O], H [auth P]	729	Neomoorella thermoacetica	Mutation(s): 0 EC: 2.3.1.169
UniProt
Find proteins for P27988 (Neomoorella thermoacetica) Explore P27988 Go to UniProtKB: P27988
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27988
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XCC Query on XCC Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	K [auth A], N [auth B], Q [auth C], T [auth D]	FE(4)-NI(1)-S(4) CLUSTER Fe₄ Ni S₄ QGLWBXDZIHZONR-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D]
SF4 (Subject of Investigation/LOI) Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain DA [auth O] SDF format, chain GA [auth P] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain S [auth D] SDF format, chain U [auth M] SDF format, chain Y [auth N] MOL2 format, chain DA [auth O] MOL2 format, chain GA [auth P] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth M] MOL2 format, chain Y [auth N] mmCIF format, chain DA [auth O] mmCIF format, chain GA [auth P] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth M] mmCIF format, chain Y [auth N]	DA [auth O] GA [auth P] I [auth A] J [auth A] M [auth B] DA [auth O], GA [auth P], I [auth A], J [auth A], M [auth B], O [auth C], P [auth C], S [auth D], U [auth M], Y [auth N]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain DA [auth O] Focus chain GA [auth P] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth M] Focus chain Y [auth N] Interactions & Density Focus chain DA [auth O] Focus chain GA [auth P] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain S [auth D] Focus chain U [auth M] Focus chain Y [auth N]
PG5 Query on PG5 Download:Ideal Coordinates CCD File SDF format, chain R [auth C] MOL2 format, chain R [auth C] mmCIF format, chain R [auth C]	R [auth C]	1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE C₈ H₁₈ O₄ YFNKIDBQEZZDLK-UHFFFAOYSA-N		Interactions Focus chain R [auth C] Interactions & Density Focus chain R [auth C]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A] mmCIF format, chain L [auth A]	L [auth A]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]
NI (Subject of Investigation/LOI) Query on NI Download:Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain EA [auth O] SDF format, chain FA [auth O] SDF format, chain HA [auth P] SDF format, chain IA [auth P] SDF format, chain V [auth M] SDF format, chain W [auth M] SDF format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain EA [auth O] MOL2 format, chain FA [auth O] MOL2 format, chain HA [auth P] MOL2 format, chain IA [auth P] MOL2 format, chain V [auth M] MOL2 format, chain W [auth M] MOL2 format, chain Z [auth N] mmCIF format, chain AA [auth N] mmCIF format, chain EA [auth O] mmCIF format, chain FA [auth O] mmCIF format, chain HA [auth P] mmCIF format, chain IA [auth P] mmCIF format, chain V [auth M] mmCIF format, chain W [auth M] mmCIF format, chain Z [auth N]	AA [auth N] EA [auth O] FA [auth O] HA [auth P] IA [auth P] AA [auth N], EA [auth O], FA [auth O], HA [auth P], IA [auth P], V [auth M], W [auth M], Z [auth N]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain EA [auth O] Focus chain FA [auth O] Focus chain HA [auth P] Focus chain IA [auth P] Focus chain V [auth M] Focus chain W [auth M] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain EA [auth O] Focus chain FA [auth O] Focus chain HA [auth P] Focus chain IA [auth P] Focus chain V [auth M] Focus chain W [auth M] Focus chain Z [auth N]
CMO (Subject of Investigation/LOI) Query on CMO Download:Ideal Coordinates CCD File SDF format, chain BA [auth N] SDF format, chain JA [auth P] SDF format, chain X [auth M] MOL2 format, chain BA [auth N] MOL2 format, chain JA [auth P] MOL2 format, chain X [auth M] mmCIF format, chain BA [auth N] mmCIF format, chain JA [auth P] mmCIF format, chain X [auth M]	BA [auth N], JA [auth P], X [auth M]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain BA [auth N] Focus chain JA [auth P] Focus chain X [auth M] Interactions & Density Focus chain BA [auth N] Focus chain JA [auth P] Focus chain X [auth M]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain CA [auth N] MOL2 format, chain CA [auth N] mmCIF format, chain CA [auth N]	CA [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth N] Interactions & Density Focus chain CA [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.47 Å
R-Value Free: 0.234 (Depositor), 0.234 (DCC)
R-Value Work: 0.203 (Depositor), 0.204 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.729	α = 101.818
b = 137.383	β = 109.077
c = 141.867	γ = 103.657

Software Package:

Software Name	Purpose
PHENIX	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: 2020-10-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM126982
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM008334
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM124165
Department of Energy (DOE, United States)	United States	DE-AC02-06CH11357