4M1E | pdb_00004m1e

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.

PDB DOI: https://doi.org/10.2210/pdb4M1E/pdb

Classification: TRANSFERASE
Organism(s): Planctopirus limnophila DSM 3776
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-08-02 Released: 2013-08-21
Deposition Author(s): Malashkevich, V.N., Bonanno, J.B., 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., Khafizov, K., Seidel, R., Almo, S.C., New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.258 (Depositor), 0.256 (DCC)
R-Value Work:
0.213 (Depositor), 0.213 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of purine nucleoside phosphorylase I from Planctomyces limnophilus DSM 3776, NYSGRC Target 029364.

Malashkevich, V.N., Bonanno, J.B., 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., Khafizov, K., Seidel, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 200.08 kDa
Atom Count: 13,263
Modeled Residue Count: 1,636
Deposited Residue Count: 1,782
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 [auth E] E [auth D] A, B, C, D [auth E], E [auth D], F	297	Planctopirus limnophila DSM 3776	Mutation(s): 0 Gene Names: Plim_2216 EC: 2.4.2.1
UniProt
Find proteins for D5SMY7 (Planctopirus limnophila (strain ATCC 43296 / DSM 3776 / IFAM 1008 / Mu 290)) Explore D5SMY7 Go to UniProtKB: D5SMY7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	D5SMY7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth E] SDF format, chain U [auth D] SDF format, chain W [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain U [auth D] MOL2 format, chain W [auth F] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain U [auth D] mmCIF format, chain W [auth F]	H [auth A] K [auth B] N [auth C] Q [auth E] U [auth D] H [auth A], K [auth B], N [auth C], Q [auth E], U [auth D], W [auth F]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth E] Focus chain U [auth D] Focus chain W [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth E] Focus chain U [auth D] Focus chain W [auth F]
6PC Query on 6PC Download:Ideal Coordinates CCD File SDF format, chain X [auth F] SDF format, chain S [auth D] SDF format, chain R [auth E] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain I [auth A] MOL2 format, chain X [auth F] MOL2 format, chain S [auth D] MOL2 format, chain R [auth E] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain I [auth A] mmCIF format, chain X [auth F] mmCIF format, chain S [auth D] mmCIF format, chain R [auth E] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain I [auth A]	I [auth A] L [auth B] O [auth C] R [auth E] S [auth D] I [auth A], L [auth B], O [auth C], R [auth E], S [auth D], X [auth F]	PYRIDINE-2-CARBOXYLIC ACID C₆ H₅ N O₂ SIOXPEMLGUPBBT-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth E] Focus chain S [auth D] Focus chain X [auth F] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth E] Focus chain S [auth D] Focus chain X [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth F] SDF format, chain T [auth D] SDF format, chain P [auth E] SDF format, chain M [auth C] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain V [auth F] MOL2 format, chain T [auth D] MOL2 format, chain P [auth E] MOL2 format, chain M [auth C] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain V [auth F] mmCIF format, chain T [auth D] mmCIF format, chain P [auth E] mmCIF format, chain M [auth C] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] M [auth C] P [auth E] T [auth D] G [auth A], J [auth B], M [auth C], P [auth E], T [auth D], V [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth E] Focus chain T [auth D] Focus chain V [auth F] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth E] Focus chain T [auth D] Focus chain V [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A B C D [auth E] E [auth D] A, B, C, D [auth E], E [auth D], F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.258 (Depositor), 0.256 (DCC)
R-Value Work: 0.213 (Depositor), 0.213 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.95	α = 103.42
b = 81.06	β = 105.36
c = 91.616	γ = 112.73

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-08-21

Deposition Author(s):

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-08-21
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 1.3: 2024-11-06
Changes: Structure summary