6VJR | pdb_00006vjr

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., Mathews, I.I., Wakatsuki, S., Kulakman, C.
Funding Organization(s): National Science Foundation (NSF, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.158 (Depositor), 0.158 (DCC)
R-Value Work:
0.126 (Depositor), 0.126 (DCC)
R-Value Observed:
0.127 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 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: 230.5 kDa
Atom Count: 18,010
Modeled 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 6 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 V [auth C] SDF format, chain N [auth B] SDF format, chain F [auth A] SDF format, chain CA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain N [auth B] MOL2 format, chain F [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain N [auth B] mmCIF format, chain F [auth A] mmCIF format, chain CA [auth D]	CA [auth D], F [auth A], N [auth B], V [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain V [auth C] Interactions & Density Focus chain CA [auth D] Focus chain F [auth A] Focus chain N [auth B] Focus chain V [auth C]
SF4 Query on SF4 Download Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain M [auth B] SDF format, chain E [auth A] SDF format, chain BA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain BA [auth D]	BA [auth D], E [auth A], M [auth B], U [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain U [auth C] Interactions & Density Focus chain BA [auth D] Focus chain E [auth A] Focus chain M [auth B] Focus chain U [auth C]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain W [auth C] SDF format, chain T [auth C] SDF format, chain O [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain DA [auth D] MOL2 format, chain W [auth C] MOL2 format, chain T [auth C] MOL2 format, chain O [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain W [auth C] mmCIF format, chain T [auth C] mmCIF format, chain O [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain DA [auth D]	DA [auth D] G [auth A] H [auth A] O [auth B] T [auth C] DA [auth D], G [auth A], H [auth A], O [auth B], T [auth C], W [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain W [auth C] Interactions & Density Focus chain DA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain O [auth B] Focus chain T [auth C] Focus chain W [auth C]
FE Query on FE Download Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain P [auth B] SDF format, chain I [auth A] SDF format, chain EA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain P [auth B] MOL2 format, chain I [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain P [auth B] mmCIF format, chain I [auth A] mmCIF format, chain EA [auth D]	EA [auth D], I [auth A], P [auth B], X [auth C]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain X [auth C] Interactions & Density Focus chain EA [auth D] Focus chain I [auth A] Focus chain P [auth B] Focus chain X [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain HA [auth D] SDF format, chain GA [auth D] SDF format, chain AA [auth C] MOL2 format, chain Z [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain Z [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain AA [auth C]	AA [auth C] GA [auth D] HA [auth D] K [auth A] L [auth A] AA [auth C], GA [auth D], HA [auth D], K [auth A], L [auth A], R [auth B], S [auth B], Z [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth D] Focus chain HA [auth D] Focus chain K [auth A] Focus chain L [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain Z [auth C]
UNL Query on UNL Download Ideal Coordinates CCD File	FA [auth D], J [auth A], Q [auth B], Y [auth C]	Unknown ligand FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain FA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain Y [auth C] Interactions & Density Focus chain FA [auth D] Focus chain J [auth A] Focus chain Q [auth B] Focus chain Y [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.158 (Depositor), 0.158 (DCC)
R-Value Work: 0.126 (Depositor), 0.126 (DCC)
R-Value Observed: 0.127 (Depositor)

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
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-01-27

Deposition Author(s):

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
Version 2.0: 2025-08-13
Type: Coordinate replacement
Reason: Model completeness
Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary