2P5Y | pdb_00002p5y

Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD

PDB DOI: https://doi.org/10.2210/pdb2P5Y/pdb

Classification: ISOMERASE
Organism(s): Thermus thermophilus HB8
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-03-16 Released: 2007-04-17
Deposition Author(s): Fu, Z.-Q., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhu, J., Swindell, J.T., Chrzas, J., Rose, J.P., Wang, B.-C., Southeast Collaboratory for Structural Genomics (SECSG), RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.207 (Depositor), 0.207 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD

Fu, Z.-Q., Chen, L., Ebihara, A., Shinkai, A., Kuramitsu, S., Yokoyama, S., Zhu, J., Swindell, J.T., Chrzas, J., Rose, J.P., Wang, B.-C.

To be published.

Macromolecule Content

Total Structure Weight: 34.48 kDa
Atom Count: 2,648
Modeled Residue Count: 311
Deposited Residue Count: 311
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UDP-glucose 4-epimerase	A	311	Thermus thermophilus HB8	Mutation(s): 0 Gene Names: TTHA0591 EC: 5.1.3.2
UniProt
Find proteins for Q5SKQ2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKQ2 Go to UniProtKB: Q5SKQ2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5SKQ2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD 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]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.207 (Depositor), 0.207 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.667	α = 90
b = 135.667	β = 90
c = 135.667	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SERGUI	data collection
HKL-2000	data reduction
EPMR	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2007-04-17

Deposition Author(s):

Southeast Collaboratory for Structural Genomics (SECSG)

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2007-04-17
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: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Database references, Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description