5U9C | pdb_00005u9c

1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica

PDB DOI: https://doi.org/10.2210/pdb5U9C/pdb

Classification: HYDROLASE,OXIDOREDUCTASE
Organism(s): Yersinia enterocolitica
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-12-15 Released: 2016-12-28
Deposition Author(s): Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Olphie, A., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.191 (Depositor), 0.197 (DCC)
R-Value Work:
0.160 (Depositor), 0.166 (DCC)
R-Value Observed:
0.161 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica.

Minasov, G., Shuvalova, L., Flores, K., Dubrovska, I., Olphie, A., Grimshaw, S., Kwon, K., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 194.35 kDa
Atom Count: 15,720
Modeled Residue Count: 1,732
Deposited Residue Count: 1,752
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dTDP-4-dehydrorhamnose Reductase	A, B, C, D, E A, B, C, D, E, F	292	Yersinia enterocolitica	Mutation(s): 0 Gene Names: wbbW EC: 1.1.1.133
UniProt
Find proteins for Q56905 (Yersinia enterocolitica) Explore Q56905 Go to UniProtKB: Q56905
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q56905
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain P [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain N [auth D]	M [auth D], N [auth D], P [auth E], Q [auth F]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F] Interactions & Density Focus chain M [auth D] Focus chain N [auth D] Focus chain P [auth E] Focus chain Q [auth F]
BDF Query on BDF Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth C] mmCIF format, chain L [auth C]	G [auth A], K [auth C], L [auth C]	beta-D-fructopyranose C₆ H₁₂ O₆ LKDRXBCSQODPBY-ARQDHWQXSA-N		Interactions Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth C] Focus chain L [auth C]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]
TRS Query on TRS Download Ideal Coordinates CCD File SDF format, chain R [auth F] MOL2 format, chain R [auth F] mmCIF format, chain R [auth F]	R [auth F]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C₄ H₁₂ N O₃ LENZDBCJOHFCAS-UHFFFAOYSA-O		Interactions Focus chain R [auth F] Interactions & Density Focus chain R [auth F]
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	H [auth A], I [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.191 (Depositor), 0.197 (DCC)
R-Value Work: 0.160 (Depositor), 0.166 (DCC)
R-Value Observed: 0.161 (Depositor)

Diffraction Data: https://doi.org/10.18430/m35u9c

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.445	α = 90
b = 184.871	β = 90
c = 187.017	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-12-28

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-12-28
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Structure summary