6HS9 | pdb_00006hs9

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

PDB DOI: https://doi.org/10.2210/pdb6HS9/pdb

Classification: BIOSYNTHETIC PROTEIN
Organism(s): Eshraghiella crossota DSM 2876
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-09-29 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: 1.05 Å
R-Value Free:
0.134 (Depositor), 0.136 (DCC)
R-Value Work:
0.113 (Depositor), 0.115 (DCC)
R-Value Observed:
0.114 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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., Ner, L., Roszak, A.W.

To be published.

Macromolecule Content

Total Structure Weight: 16.56 kDa
Atom Count: 1,471
Modeled Residue Count: 145
Deposited Residue Count: 145
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-dehydroquinate dehydratase	A	145	Eshraghiella crossota DSM 2876	Mutation(s): 0 Gene Names: aroQ, BUTYVIB_01550 EC: 4.2.1.10
UniProt
Find proteins for D4S0D1 (Eshraghiella crossota DSM 2876) Explore D4S0D1 Go to UniProtKB: D4S0D1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D4S0D1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3DS Query on 3DS Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(4S,5R)-4,5-dihydroxy-3-oxocyclohex-1-ene-1-carboxylic acid C₇ H₈ O₅ SLWWJZMPHJJOPH-PHDIDXHHSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.05 Å
R-Value Free: 0.134 (Depositor), 0.136 (DCC)
R-Value Work: 0.113 (Depositor), 0.115 (DCC)
R-Value Observed: 0.114 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.55	α = 90
b = 79.55	β = 90
c = 72.28	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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

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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.