4UC0 | pdb_00004uc0

Crystal Structure Of a purine nucleoside phosphorylase (PSI-NYSGRC-029736) from Agrobacterium vitis

PDB DOI: https://doi.org/10.2210/pdb4UC0/pdb

Classification: TRANSFERASE
Organism(s): Gillisella vitis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2014-08-13 Released: 2014-10-08
Deposition Author(s): Cameron, S.A., Sampathkumar, P., Ramagopal, U.A., Attonito, J., Ahmed, M., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Glenn, A.S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Wasserman, S.R., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.224 (Depositor), 0.224 (DCC)
R-Value Work:
0.179 (Depositor), 0.179 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure Of a purine nucleoside phosphorylase (PSI-NYSGRC-029736) from Agrobacterium vitis

Cameron, S.A., Sampathkumar, P., Ramagopal, U.A., Attonito, J., Ahmed, M., Bhosle, R., Bonanno, J., Chamala, S., Chowdhury, S., Glenn, A.S., Hammonds, J., Hillerich, B., Love, J.D., Seidel, R., Stead, M., Toro, R., Wasserman, S.R., Schramm, V.L., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

To be published.

Macromolecule Content

Total Structure Weight: 31.46 kDa
Atom Count: 1,834
Modeled Residue Count: 247
Deposited Residue Count: 291
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase	A	291	Gillisella vitis	Mutation(s): 0 Gene Names: Avi_0263 EC: 2.4.2.1
UniProt
Find proteins for B9JYS2 (Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)) Explore B9JYS2 Go to UniProtKB: B9JYS2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9JYS2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HPA Query on HPA 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]	HYPOXANTHINE C₅ H₄ N₄ O FDGQSTZJBFJUBT-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.224 (Depositor), 0.224 (DCC)
R-Value Work: 0.179 (Depositor), 0.179 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.881	α = 90
b = 97.881	β = 90
c = 46.356	γ = 120

Software Package:

Software Name	Purpose
HKL-3000	data reduction
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
REFMAC	refinement

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2014-10-08

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2014-10-08
Type: Initial release
Version 1.1: 2019-12-04
Changes: Author supporting evidence, Data collection, Derived calculations, Other, Source and taxonomy
Version 1.2: 2023-12-27
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary