4MZY | pdb_00004mzy

Crystal structure of enterococcus faecalis nicotinate phosphoribosyltransferase with malonate and phosphate bound

PDB DOI: https://doi.org/10.2210/pdb4MZY/pdb

Classification: TRANSFERASE
Organism(s): Enterococcus faecalis V583
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2013-09-30 Released: 2013-10-23
Deposition Author(s): Patskovsky, Y., Toro, R., Wasserman, S.R., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC), New York Structural Genomics Research Consortium (NYSGRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.186 (Depositor), 0.200 (DCC)
R-Value Work:
0.154 (Depositor), 0.170 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure of Enterococcus Faecalis Nicotinate Phosphoribosyltransferase

Patskovsky, Y., Toro, R., Wasserman, S.R., Burley, S.K., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 58.4 kDa
Atom Count: 4,252
Modeled Residue Count: 486
Deposited Residue Count: 494
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NICOTINATE PHOSPHORIBOSYLTRANSFERASE	A	494	Enterococcus faecalis V583	Mutation(s): 1 Gene Names: EF2626 EC: 2.4.2.11 (PDB Primary Data), 6.3.4.21 (UniProt)
UniProt
Find proteins for Q830Y8 (Enterococcus faecalis (strain ATCC 700802 / V583)) Explore Q830Y8 Go to UniProtKB: Q830Y8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q830Y8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLA Query on MLA Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	P [auth A], Q [auth A], R [auth A]	MALONIC ACID C₃ H₄ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain U [auth A] MOL2 format, chain U [auth A] mmCIF format, chain U [auth A]	U [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Interactions & Density Focus chain U [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A]	S [auth A], T [auth A], V [auth A], W [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain W [auth A] Interactions & Density Focus chain S [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain W [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.186 (Depositor), 0.200 (DCC)
R-Value Work: 0.154 (Depositor), 0.170 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.254	α = 90
b = 111.381	β = 90
c = 154.604	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2013-10-23

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

New York Structural Genomics Research Consortium (NYSGRC)

Revision History (Full details and data files)

Version 1.0: 2013-10-23
Type: Initial release
Version 1.1: 2013-11-27
Changes: Structure summary
Version 1.2: 2015-04-29
Changes: Non-polymer description
Version 1.3: 2021-02-10
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2023-09-20
Changes: Data collection, Database references, Refinement description