3LXY

Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Yersinia pestis CO92

PDB DOI: https://doi.org/10.2210/pdb3LXY/pdb

Classification: OXIDOREDUCTASE
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-02-25 Released: 2010-03-09
Deposition Author(s): Nocek, B., Maltseva, N., Kwon, K., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases, Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248
R-Value Work: 0.192
R-Value Observed: 0.194

wwPDB Validation 3D Report Full Report

This is version 2.1 of the entry. See complete history.

Literature

Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Yersinia pestis CO92

Nocek, B., Maltseva, N., Kwon, K., Makowska-Grzyska, M., Anderson, W., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 36.07 kDa
Atom Count: 2,681
Modelled Residue Count: 329
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxythreonine-4-phosphate dehydrogenase	A	334	Yersinia pestis	Mutation(s): 0 Gene Names: pdxA, YPO0493, y3682, YP_3686 EC: 1.1.1.262
UniProt
Find proteins for P58719 (Yersinia pestis) Explore P58719 Go to UniProtKB: P58719
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P58719
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	B	2		N/A	Interactions Focus chain B Interactions & Density Focus chain B
Glycosylation Resources
GlyTouCan: G05551OP GlyCosmos: G05551OP

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NI Query on NI Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003 Query on PRD_900003	B	sucrose	Oligosaccharide / Nutrient		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.248
R-Value Work: 0.192
R-Value Observed: 0.194
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M33LXY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.939	α = 90
b = 88.105	β = 90
c = 100.511	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2011-12-14
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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3LXY

Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Yersinia pestis CO92

Crystal structure of 4-hydroxythreonine-4-phosphate dehydrogenase from Yersinia pestis CO92

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources

Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)