3BR8 | pdb_00003br8

Crystal structure of acylphosphatase from Bacillus subtilis

PDB DOI: https://doi.org/10.2210/pdb3BR8/pdb

Classification: HYDROLASE
Organism(s): Bacillus subtilis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-12-21 Released: 2008-06-24
Deposition Author(s): Li, D., Hu, J.C., Xia, B., Su, X.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free:
0.225 (Depositor), 0.211 (DCC)
R-Value Work:
0.190 (Depositor), 0.179 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3BR8

This is version 1.3 of the entry. See complete history.

Literature

Conformational Transitions Revealed by Structures of Acylphosphatase from Bacillus subtilis in Different States

Hu, J.C., Li, D., Su, X.D., Jin, C.W., Xia, B.

To be published.

Macromolecule Content

Total Structure Weight: 10.52 kDa
Atom Count: 828
Modeled Residue Count: 90
Deposited Residue Count: 91
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable acylphosphatase	A	91	Bacillus subtilis	Mutation(s): 0 Gene Names: yflL EC: 3.6.1.7
UniProt
Find proteins for O35031 (Bacillus subtilis (strain 168)) Explore O35031 Go to UniProtKB: O35031
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O35031
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 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]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.33 Å
R-Value Free: 0.225 (Depositor), 0.211 (DCC)
R-Value Work: 0.190 (Depositor), 0.179 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.857	α = 90
b = 48.27	β = 90
c = 59.567	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
CNS	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-06-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2024-03-13
Changes: Data collection, Database references, Derived calculations

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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.