3ODG

crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis

PDB DOI: https://doi.org/10.2210/pdb3ODG/pdb

Classification: TRANSFERASE
Organism(s): Yersinia pseudotuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-08-11 Released: 2010-08-25
Deposition Author(s): Kim, J., Ramagopal, U.A., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 ?
R-Value Free: 0.187
R-Value Work: 0.155
R-Value Observed: 0.157

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis

Kim, J., Ramagopal, U.A., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 31.13 kDa
Atom Count: 2,331
Modelled Residue Count: 273
Deposited Residue Count: 287
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Xanthosine phosphorylase	A	287	Yersinia pseudotuberculosis	Mutation(s): 0 Gene Names: pndA, xapA, YPTB1201 EC: 2.4.2 (PDB Primary Data), 2.4.2.1 (UniProt)
UniProt
Find proteins for Q66D48 (Yersinia pseudotuberculosis serotype I (strain IP32953)) Explore Q66D48 Go to UniProtKB: Q66D48
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q66D48
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
XAN Query on XAN 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]	XANTHINE C₅ H₄ N₄ O₂ LRFVTYWOQMYALW-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
CL Query on CL 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]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 ?
R-Value Free: 0.187
R-Value Work: 0.155
R-Value Observed: 0.157
Space Group: P 6₃

Unit Cell:

Length ( ? )	Angle ( ? )
a = 96.47	α = 90
b = 96.47	β = 90
c = 48.906	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-08-25

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-08-25
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-02-10
Changes: Derived calculations, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description

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3ODG

crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis

crystal structure of xanthosine phosphorylase bound with xanthine from Yersinia pseudotuberculosis

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)