6VJR

Oxygen tolerant Archeal 4hydroxybutyrylCoA dehydratase (4HBD) from N. maritimus

PDB DOI: https://doi.org/10.2210/pdb6VJR/pdb

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

Deposited: 2020-01-17 Released: 2021-01-27
Deposition Author(s): DeMirci, H.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.175
R-Value Work: 0.158
R-Value Observed: 0.158

wwPDB Validation 3D Report Full Report

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

Literature

Structural adaptation of oxygen tolerance in a key archaeal carbon fixation enzyme

Demirci, H., Wakatsuki, S.

To be published.

Macromolecule Content

Total Structure Weight: 229.99 kDa
Atom Count: 18,155
Modelled Residue Count: 2,003
Deposited Residue Count: 2,008
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vinylacetyl-CoA Delta-isomerase	A, B, C, D	502	Nitrosopumilus maritimus SCM1	Mutation(s): 0 Gene Names: Nmar_0207 EC: 5.3.3.3
UniProt
Find proteins for A9A1Y2 (Nitrosopumilus maritimus (strain SCM1)) Explore A9A1Y2 Go to UniProtKB: A9A1Y2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A9A1Y2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain F [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D]	F [auth A], M [auth B], Q [auth C], T [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain M [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 E [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D]	E [auth A], L [auth B], P [auth C], S [auth D]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain N [auth B]	G [auth A], H [auth A], I [auth A], N [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain N [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain J [auth A] MOL2 format, chain J [auth A]	J [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain J [auth A] Interactions & Density Focus chain J [auth A]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain K [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D]	K [auth A], O [auth B], R [auth C], U [auth D]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.175
R-Value Work: 0.158
R-Value Observed: 0.158
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.53	α = 90
b = 72.954	β = 98.38
c = 180.517	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

DeMirci, H.

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

Revision History (Full details and data files)

Version 1.0: 2021-01-27
Type: Initial release
Version 1.1: 2023-10-11
Changes: Advisory, Data collection, Database references, Refinement description

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Help and Resources

6VJR

Oxygen tolerant Archeal 4hydroxybutyrylCoA dehydratase (4HBD) from N. maritimus

Structural adaptation of oxygen tolerance in a key archaeal carbon fixation enzyme

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)