6HSQ | pdb_00006hsq

The crystal structure of type II Dehydroquinase from Psychromonas ingrahamii 37 crystal form 1

PDB DOI: https://doi.org/10.2210/pdb6HSQ/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Psychromonas ingrahamii 37
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-01 Released: 2019-10-23
Deposition Author(s): Lapthorn, A.J., Roszak, A.W.
Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free:
0.186 (Depositor), 0.198 (DCC)
R-Value Work:
0.168 (Depositor)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 6HSQ

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

Literature

The crystal structure of type II Dehydroquinase from Butyrivibrio crossotus DSM 2876

Lapthorn, A.J., Koyroytsaltis-McQuire, D., Roszak, A.W.

To be published.

Macromolecule Content

Total Structure Weight: 68.35 kDa
Atom Count: 5,376
Modeled Residue Count: 600
Deposited Residue Count: 608
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A, B, C, D	152	Psychromonas ingrahamii 37	Mutation(s): 0 Gene Names: aroQ, Ping_3121 EC: 4.2.1.10
UniProt
Find proteins for A1SZA3 (Psychromonas ingrahamii (strain DSM 17664 / CCUG 51855 / 37)) Explore A1SZA3 Go to UniProtKB: A1SZA3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1SZA3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A] F [auth A] H [auth B] I [auth B] K [auth C] E [auth A], F [auth A], H [auth B], I [auth B], K [auth C], L [auth C], N [auth D], O [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain N [auth D] Focus chain O [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain P [auth D] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain P [auth D] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain P [auth D] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A], J [auth B], M [auth C], P [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.46 Å
R-Value Free: 0.186 (Depositor), 0.198 (DCC)
R-Value Work: 0.168 (Depositor)
R-Value Observed: 0.169 (Depositor)

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.386	α = 90
b = 139.386	β = 90
c = 139.386	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-10-23

Deposition Author(s):

Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/P00086X/1

Revision History (Full details and data files)

Version 1.0: 2019-10-23
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.