5CVT | pdb_00005cvt

Structure of a single tryptophan mutant of Acetobacter aceti PurE containing 5-fluorotryptophan, pH 5.4

PDB DOI: https://doi.org/10.2210/pdb5CVT/pdb

Classification: ISOMERASE
Organism(s): Acetobacter aceti 1023
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2015-07-27 Released: 2016-08-10
Deposition Author(s): Sullivan, K.L., Kappock, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.155 (Depositor), 0.158 (DCC)
R-Value Work:
0.143 (Depositor), 0.146 (DCC)
R-Value Observed:
0.143 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of a single tryptophan mutant of Acetobacter aceti PurE

Sullivan, K.L., Tranchimand, S., Kappock, T.J.

To be published.

Macromolecule Content

Total Structure Weight: 38.38 kDa
Atom Count: 2,725
Modeled Residue Count: 322
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N5-carboxyaminoimidazole ribonucleotide mutase	A, B	183	Acetobacter aceti 1023	Mutation(s): 2 Gene Names: purE, AZ09_02690 EC: 5.4.99.18

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGF Query on PGF Download:Ideal Coordinates CCD File SDF format, chain H [auth B] MOL2 format, chain H [auth B] mmCIF format, chain H [auth B]	H [auth B]	2,5,8,11-TETRAOXATRIDECANE C₉ H₂₀ O₄ JRRDISHSXWGFRF-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FTR Query on FTR	A, B	L-PEPTIDE LINKING	C₁₁ H₁₁ F N₂ O₂		TRP

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.155 (Depositor), 0.158 (DCC)
R-Value Work: 0.143 (Depositor), 0.146 (DCC)
R-Value Observed: 0.143 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.695	α = 90
b = 98.695	β = 90
c = 165.057	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-08-10

Deposition Author(s):

Sullivan, K.L.

Kappock, T.J.

Revision History (Full details and data files)

Version 1.0: 2016-08-10
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description