5BOS | pdb_00005bos

Structure of Acetobacter aceti PurE-S57C, partly oxidized form

PDB DOI: https://doi.org/10.2210/pdb5BOS/pdb

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

Deposited: 2015-05-27 Released: 2016-06-15
Deposition Author(s): Sullivan, K.L., Kappock, T.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.161 (Depositor), 0.164 (DCC)
R-Value Work:
0.135 (Depositor), 0.138 (DCC)
R-Value Observed:
0.136 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 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: 38.24 kDa
Atom Count: 2,922
Modeled Residue Count: 321
Deposited Residue Count: 366
Unique protein chains: 2

Macromolecules

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| 3D Structure

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

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
N5-carboxyaminoimidazole ribonucleotide mutase	B	183	Acetobacter aceti 1023	Mutation(s): 1 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
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth B] Interactions & Density Focus chain H [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain E [auth B] MOL2 format, chain G [auth B] MOL2 format, chain E [auth B] mmCIF format, chain G [auth B] mmCIF format, chain E [auth B]	E [auth B], G [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain G [auth B] Interactions & Density Focus chain E [auth B] Focus chain G [auth B]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
OCS Query on OCS	A	L-PEPTIDE LINKING	C₃ H₇ N O₅ S		CYS
CSX Query on CSX	B	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.161 (Depositor), 0.164 (DCC)
R-Value Work: 0.135 (Depositor), 0.138 (DCC)
R-Value Observed: 0.136 (Depositor)

Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.584	α = 90
b = 99.584	β = 90
c = 164.702	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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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-06-15

Deposition Author(s):

Sullivan, K.L.

Kappock, T.J.

Revision History (Full details and data files)

Version 1.0: 2016-06-15
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection