2GQT

Crystal Structure of UDP-N-Acetylenolpyruvylglucosamine Reductase (MurB) from Thermus caldophilus

PDB DOI: https://doi.org/10.2210/pdb2GQT/pdb

Classification: OXIDOREDUCTASE
Organism(s): Thermus caldophilus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2006-04-21 Released: 2006-12-19
Deposition Author(s): Kim, M.-K., Eom, S.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.209
R-Value Work: 0.187
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Thermus caldophilus

Kim, M.-K., Cho, M.K., Song, H.-E., Kim, D., Park, B.-H., Lee, J.H., Kang, G.B., Kim, S.H., Im, Y.J., Lee, D.-S., Eom, S.H.

(2006) Proteins 66: 751-754

PubMed: 17120230 Search on PubMed
DOI: https://doi.org/10.1002/prot.21174
Primary Citation of Related Structures:
2GQT, 2GQU

Organizational Affiliation

Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 500-712, Korea.

Macromolecule Content

Total Structure Weight: 30.45 kDa
Atom Count: 2,551
Modelled Residue Count: 267
Deposited Residue Count: 268
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-N-Acetylenolpyruvylglucosamine Reductase	A	268	Thermus caldophilus	Mutation(s): 0 EC: 1.1.1.158
UniProt
Find proteins for Q5SJC8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJC8 Go to UniProtKB: Q5SJC8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q5SJC8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.209
R-Value Work: 0.187
R-Value Observed: 0.189
Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.717	α = 64.83
b = 46.501	β = 77.04
c = 48.714	γ = 84.4

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-19

Deposition Author(s):

Kim, M.-K.

Eom, S.H.

Revision History (Full details and data files)

Version 1.0: 2006-12-19
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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2GQT

Crystal Structure of UDP-N-Acetylenolpyruvylglucosamine Reductase (MurB) from Thermus caldophilus

Crystal structure of UDP-N-acetylenolpyruvylglucosamine reductase (MurB) from Thermus caldophilus

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)