6HSA | pdb_00006hsa

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

PDB DOI: https://doi.org/10.2210/pdb6HSA/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: 0.92 Å
R-Value Free:
0.120 (Depositor), 0.142 (DCC)
R-Value Work:
0.101 (Depositor), 0.129 (DCC)
R-Value Observed:
0.102 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.1 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: 17.17 kDa
Atom Count: 1,571
Modeled Residue Count: 145
Deposited Residue Count: 145
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ETE Query on ETE 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]	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C₉ H₂₀ O₅ ZNYRFEPBTVGZDN-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FLC Query on FLC Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
SER Query on SER Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SERINE C₃ H₇ N O₃ MTCFGRXMJLQNBG-REOHCLBHSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.92 Å
R-Value Free: 0.120 (Depositor), 0.142 (DCC)
R-Value Work: 0.101 (Depositor), 0.129 (DCC)
R-Value Observed: 0.102 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.476	α = 90
b = 79.476	β = 90
c = 72.033	γ = 120

Software Package:

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

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):

Lapthorn, A.J.

Roszak, A.W.

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 2.0: 2019-10-30
Changes: Advisory, Atomic model, Data collection, Derived calculations
Version 2.1: 2024-01-24
Changes: Data collection, Database references, Refinement description