4YCB

Structure of a single tryptophan mutant of Acetobacter aceti PurE

PDB DOI: https://doi.org/10.2210/pdb4YCB/pdb

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

Deposited: 2015-02-19 Released: 2016-02-24
Deposition Author(s): Kappock, T.J., Sullivan, K.L., Mullins, E.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.149
R-Value Work: 0.140
R-Value Observed: 0.141

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 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: 38.4 kDa
Atom Count: 2,959
Modelled Residue Count: 322
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PGF Query on PGF Download Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	2,5,8,11-TETRAOXATRIDECANE C₉ H₂₀ O₄ JRRDISHSXWGFRF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B]	F [auth A], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Focus chain L [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	D [auth A], E [auth A], H [auth B], I [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth B] Focus chain I [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain J [auth B] MOL2 format, chain J [auth B] mmCIF format, chain J [auth B]	J [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Interactions & Density Focus chain J [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.149
R-Value Work: 0.140
R-Value Observed: 0.141
Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.803	α = 90
b = 99.803	β = 90
c = 164.409	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-02-24

Deposition Author(s):

Kappock, T.J.

Sullivan, K.L.

Mullins, E.A.

Revision History (Full details and data files)

Version 1.0: 2016-02-24
Type: Initial release
Version 1.1: 2016-06-01
Changes: Other
Version 1.2: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description