8WZU | pdb_00008wzu

4-hydroxybutyryl-CoA Synthetase (ADP-forming) from Nitrosopumilus maritimus.

PDB DOI: https://doi.org/10.2210/pdb8WZU/pdb
Entry: 8WZU supersedes: 8IUP

Classification: LIGASE
Organism(s): Nitrosopumilus maritimus SCM1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-11-02 Released: 2024-06-12
Deposition Author(s): Johnson, J., Demirci, H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.280 (Depositor), 0.279 (DCC)
R-Value Work:
0.236 (Depositor), 0.239 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of 4-hydroxybutyryl CoA synthetase (ADP-forming): A Key Enzyme in the Thaumarchaeal Hydroxypropionate/Hydroxybutyrate cycle.

Johnson, J., Demirci, H.

To be published.

Macromolecule Content

Total Structure Weight: 151.65 kDa
Atom Count: 9,578
Modelled Residue Count: 1,249
Deposited Residue Count: 1,396
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxybutyrate--CoA ligase [ADP-forming]	A, B	698	Nitrosopumilus maritimus SCM1	Mutation(s): 0 Gene Names: Nmar_0206 EC: 6.2.1.56
UniProt
Find proteins for A9A1Y1 (Nitrosopumilus maritimus (strain SCM1)) Explore A9A1Y1 Go to UniProtKB: A9A1Y1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9A1Y1
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		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: 2.80 Å
R-Value Free: 0.280 (Depositor), 0.279 (DCC)
R-Value Work: 0.236 (Depositor), 0.239 (DCC)
R-Value Observed: 0.239 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 356.98	α = 90
b = 70.4	β = 90
c = 75.81	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-12

Deposition Author(s):

This entry supersedes: 8IUP

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1231306

Revision History (Full details and data files)

Version 1.0: 2024-06-12
Type: Initial release
Version 1.1: 2025-03-12
Changes: Database references, Structure summary

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.