1W7F | pdb_00001w7f

Crystal structure of the class A beta-lactamase BS3 inhibited with isocitrate

PDB DOI: https://doi.org/10.2210/pdb1W7F/pdb

Classification: HYDROLASE
Organism(s): Bacillus licheniformis
Mutation(s): No

Deposited: 2004-09-01 Released: 2006-05-24
Deposition Author(s): Petrella, S., Sauvage, E., Herman, R., Charlier, P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free:
0.253 (Depositor), 0.248 (DCC)
R-Value Work:
0.208 (Depositor), 0.203 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1W7F

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of the Class a Beta-Lactamase Bs3 Bs3 Inhibited with Isocitrate

Petrella, S., Sauvage, E., Herman, R., Charlier, P.

To be published.

Macromolecule Content

Total Structure Weight: 68.22 kDa
Atom Count: 4,215
Modeled Residue Count: 512
Deposited Residue Count: 614
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE	A, B	307	Bacillus licheniformis	Mutation(s): 0 EC: 3.5.2.6
UniProt
Find proteins for P00808 (Bacillus licheniformis) Explore P00808 Go to UniProtKB: P00808
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00808
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ICT Query on ICT 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]	ISOCITRIC ACID C₆ H₈ O₇ ODBLHEXUDAPZAU-ZAFYKAAXSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.253 (Depositor), 0.248 (DCC)
R-Value Work: 0.208 (Depositor), 0.203 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.896	α = 90
b = 104.655	β = 94.33
c = 63.766	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2006-05-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-05-24
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.