4YI7 | pdb_00004yi7

Anthranilate bound at active site of anthranilate phosphoribosyl transferase from Acinetobacter (AnPRT; TrpD)

PDB DOI: https://doi.org/10.2210/pdb4YI7/pdb

Classification: TRANSFERASE
Organism(s): Acinetobacter baylyi ADP1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-02-28 Released: 2015-09-02
Deposition Author(s): Evans, G.L., Newton, M.S., Norris, G.E., Patrick, W.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.258 (Depositor), 0.263 (DCC)
R-Value Work:
0.223 (Depositor), 0.233 (DCC)
R-Value Observed:
0.225 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history.

Literature

Substrate inhibition of protein in tryptophan biosynthesis pathway redirects flux to aromatic catabolism in Acinetobacter baylyi ADP1.

Evans, G.E., Nigon, L.V., Ponniah, K., Burr, N., Anderson, B.F., Norris, G.E., Patrick, W.M.

To be published.

Macromolecule Content

Total Structure Weight: 39.59 kDa
Atom Count: 2,460
Modeled Residue Count: 331
Deposited Residue Count: 365
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate phosphoribosyltransferase	A	365	Acinetobacter baylyi ADP1	Mutation(s): 0 Gene Names: trpD, ACIAD2462 EC: 2.4.2.18
UniProt
Find proteins for P00500 (Acinetobacter baylyi (strain ATCC 33305 / BD413 / ADP1)) Explore P00500 Go to UniProtKB: P00500
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00500
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BE2 Query on BE2 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]	2-AMINOBENZOIC ACID C₇ H₇ N O₂ RWZYAGGXGHYGMB-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.258 (Depositor), 0.263 (DCC)
R-Value Work: 0.223 (Depositor), 0.233 (DCC)
R-Value Observed: 0.225 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.997	α = 90
b = 70.83	β = 90
c = 169.156	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-09-02
Type: Initial release
Version 1.1: 2015-12-09
Changes: Database references
Version 1.2: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Refinement description
Version 2.0: 2023-11-15
Changes: Atomic model, Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.