6HZI | pdb_00006hzi

Apo structure of TP domain from Burkholderia pseudomallei penicillin-binding protein 3

PDB DOI: https://doi.org/10.2210/pdb6HZI/pdb

Classification: PEPTIDE BINDING PROTEIN
Organism(s): Burkholderia pseudomallei
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-10-23 Released: 2019-11-20
Deposition Author(s): Bellini, D., Koekemoer, L., Newman, H., Dowson, C.G.
Funding Organization(s): Medical Research Council (United Kingdom)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Work:
0.196 (Depositor), 0.204 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Apo structure of TP domain from Burkholderia pseudomallei penicillin-binding protein 3

Bellini, D., Koekemoer, L., Newman, H., Dowson, C.G.

To be published.

Macromolecule Content

Total Structure Weight: 39.75 kDa
Atom Count: 2,550
Modeled Residue Count: 331
Deposited Residue Count: 374
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidoglycan D,D-transpeptidase FtsI	A	374	Burkholderia pseudomallei	Mutation(s): 0 Gene Names: ftsI, CXQ84_03210, DP46_2053 EC: 3.4.16.4
UniProt
Find proteins for Q63QJ1 (Burkholderia pseudomallei (strain K96243)) Explore Q63QJ1 Go to UniProtKB: Q63QJ1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q63QJ1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Work: 0.196 (Depositor), 0.204 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.394	α = 90
b = 106.394	β = 90
c = 95.678	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
MrBUMP	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	grant.MR/P007503/1

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description

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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.