3OCC | pdb_00003occ

Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

PDB DOI: https://doi.org/10.2210/pdb3OCC/pdb

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

Deposited: 2010-08-09 Released: 2010-11-10
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: 1.70 Å
R-Value Free:
0.181 (Depositor), 0.188 (DCC)
R-Value Work:
0.149 (Depositor), 0.156 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

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

To be published.

Macromolecule Content

Total Structure Weight: 157.96 kDa
Atom Count: 12,217
Modeled Residue Count: 1,424
Deposited Residue Count: 1,434
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Purine nucleoside phosphorylase deoD-type	A, B, C, D, E A, B, C, D, E, F	239	Yersinia pseudotuberculosis YPIII	Mutation(s): 0 Gene Names: deoD, YPK_3624 EC: 2.4.2.1
UniProt
Find proteins for B1JL34 (Yersinia pseudotuberculosis serotype O:3 (strain YPIII)) Explore B1JL34 Go to UniProtKB: B1JL34
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B1JL34
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DIH Query on DIH Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain Q [auth F] SDF format, chain K [auth C] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain K [auth C] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain Q [auth F] mmCIF format, chain K [auth C]	G [auth A] I [auth B] K [auth C] M [auth D] O [auth E] G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	7-[[(3R,4R)-3-(hydroxymethyl)-4-oxidanyl-pyrrolidin-1-ium-1-yl]methyl]-3,5-dihydropyrrolo[3,2-d]pyrimidin-4-one C₁₂ H₁₇ N₄ O₃ AFNHHLILYQEHKK-BDAKNGLRSA-O		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth C] Focus chain M [auth D] Focus chain O [auth E] Focus chain Q [auth F]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain R [auth F] SDF format, chain P [auth E] SDF format, chain N [auth D] SDF format, chain L [auth C] SDF format, chain J [auth B] SDF format, chain H [auth A] MOL2 format, chain R [auth F] MOL2 format, chain P [auth E] MOL2 format, chain N [auth D] MOL2 format, chain L [auth C] MOL2 format, chain J [auth B] MOL2 format, chain H [auth A] mmCIF format, chain R [auth F] mmCIF format, chain P [auth E] mmCIF format, chain N [auth D] mmCIF format, chain L [auth C] mmCIF format, chain J [auth B] mmCIF format, chain H [auth A]	H [auth A] J [auth B] L [auth C] N [auth D] P [auth E] H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F] Interactions & Density Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth C] Focus chain N [auth D] Focus chain P [auth E] Focus chain R [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.181 (Depositor), 0.188 (DCC)
R-Value Work: 0.149 (Depositor), 0.156 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.647	α = 90
b = 109.829	β = 90
c = 154.747	γ = 90

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

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Entry History

Deposition Data

Released Date: 2010-11-10

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2010-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 2.0: 2018-12-12
Changes: Advisory, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 2.2: 2023-09-06
Changes: Data collection, Database references, Refinement description

3OCC | pdb_00003occ

Crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

Literature

crystal structure of PNP with DADMEimmH from Yersinia pseudotuberculosis

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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