4Z7J | pdb_00004z7j

Structure of Acetobacter aceti PurE-S57A

PDB DOI: https://doi.org/10.2210/pdb4Z7J/pdb

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

Deposited: 2015-04-07 Released: 2016-04-13
Deposition Author(s): Kappock, T.J., Sullivan, K.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.157 (Depositor), 0.157 (DCC)
R-Value Work:
0.139 (Depositor), 0.141 (DCC)
R-Value Observed:
0.140 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Mutation of the conserved serine in two PurE classes

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

To be published.

Macromolecule Content

Total Structure Weight: 38.61 kDa
Atom Count: 2,896
Modeled Residue Count: 319
Deposited Residue Count: 366
Unique protein chains: 1

Macromolecules

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| 3D Structure

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RP5 Query on RP5 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	5-O-phosphono-beta-D-ribofuranose C₅ H₁₁ O₈ P KTVPXOYAKDPRHY-TXICZTDVSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
PG0 Query on PG0 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-(2-METHOXYETHOXY)ETHANOL C₅ H₁₂ O₃ SBASXUCJHJRPEV-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 L [auth B] MOL2 format, chain L [auth B] mmCIF format, chain L [auth B]	L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A]	E [auth A], F [auth A], J [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B]
BCT Query on BCT Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain D [auth A]	D [auth A], I [auth B]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain C [auth A] MOL2 format, chain H [auth B] MOL2 format, chain C [auth A] mmCIF format, chain H [auth B] mmCIF format, chain C [auth A]	C [auth A], H [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.157 (Depositor), 0.157 (DCC)
R-Value Work: 0.139 (Depositor), 0.141 (DCC)
R-Value Observed: 0.140 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.362	α = 90
b = 99.362	β = 90
c = 165.353	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

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Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Kappock, T.J.

Sullivan, K.L.

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations
Version 2.1: 2023-09-27
Changes: Data collection, Database references, Refinement description, Structure summary