4NS1 | pdb_00004ns1

Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC 33277, NYSGRC Target 30972

PDB DOI: https://doi.org/10.2210/pdb4NS1/pdb

Classification: TRANSFERASE
Organism(s): Porphyromonas gingivalis ATCC 33277
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-11-27 Released: 2013-12-25
Deposition Author(s): Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R., Bonanno, J.B., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free:
0.186 (Depositor), 0.186 (DCC)
R-Value Work:
0.171 (Depositor), 0.171 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of purine nucleoside phosphorylase from Porphyromonas gingivalis ATCC 33277, NYSGRC Target 30972.

Malashkevich, V.N., Bhosle, R., Toro, R., Hillerich, B., Gizzi, A., Garforth, S., Kar, A., Chan, M.K., Lafluer, J., Patel, H., Matikainen, B., Chamala, S., Lim, S., Celikgil, A., Villegas, G., Evans, B., Love, J., Fiser, A., Seidel, R., Bonanno, J.B., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 134.18 kDa
Atom Count: 9,991
Modeled Residue Count: 1,074
Deposited Residue Count: 1,180
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, B, C, D	295	Porphyromonas gingivalis ATCC 33277	Mutation(s): 0 Gene Names: PGN_1412 EC: 2.4.2.1
UniProt
Find proteins for B2RKN6 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)) Explore B2RKN6 Go to UniProtKB: B2RKN6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2RKN6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D5M Query on D5M Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain P [auth C] SDF format, chain K [auth B] SDF format, chain E [auth A] MOL2 format, chain U [auth D] MOL2 format, chain P [auth C] MOL2 format, chain K [auth B] MOL2 format, chain E [auth A] mmCIF format, chain U [auth D] mmCIF format, chain P [auth C] mmCIF format, chain K [auth B] mmCIF format, chain E [auth A]	E [auth A], K [auth B], P [auth C], U [auth D]	2'-DEOXYADENOSINE-5'-MONOPHOSPHATE C₁₀ H₁₄ N₅ O₆ P KHWCHTKSEGGWEX-RRKCRQDMSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain P [auth C] Focus chain U [auth D]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain L [auth B] SDF format, chain J [auth A] SDF format, chain F [auth A] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain L [auth B] MOL2 format, chain J [auth A] MOL2 format, chain F [auth A] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain L [auth B] mmCIF format, chain J [auth A] mmCIF format, chain F [auth A]	F [auth A] J [auth A] L [auth B] Q [auth C] V [auth D] F [auth A], J [auth A], L [auth B], Q [auth C], V [auth D], W [auth D], X [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain J [auth A] Focus chain L [auth B] Focus chain Q [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] M [auth B] N [auth B] G [auth A], H [auth A], I [auth A], M [auth B], N [auth B], O [auth B], R [auth C], S [auth C], T [auth C], Y [auth D], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO Query on CSO	A, B, C, D	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.64 Å
R-Value Free: 0.186 (Depositor), 0.186 (DCC)
R-Value Work: 0.171 (Depositor), 0.171 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 218.904	α = 90
b = 218.904	β = 90
c = 218.904	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-3000	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-12-25

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-12-25
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-12-06
Changes: Data collection
Version 2.0: 2024-05-29
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description
Version 2.1: 2024-11-06
Changes: Structure summary