6I1G | pdb_00006i1g

Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with piperacillin

PDB DOI: https://doi.org/10.2210/pdb6I1G/pdb

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

Deposited: 2018-10-28 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: 2.13 Å
R-Value Free:
0.284 (Depositor), 0.270 (DCC)
R-Value Work:
0.240 (Depositor), 0.230 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of TP domain from Chlamydia trachomatis Penicillin-Binding Protein 3 in complex with piperacillin

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

To be published.

Macromolecule Content

Total Structure Weight: 73.97 kDa
Atom Count: 5,023
Modeled Residue Count: 666
Deposited Residue Count: 692
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-binding protein,Penicillin-binding protein	A, B	346	Chlamydia trachomatis	Mutation(s): 0 Gene Names: pbp_2, ERS133248_00492 EC: 2.4.1.129
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
JPP (Subject of Investigation/LOI) Query on JPP Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	Piperacillin (Open Form) C₂₃ H₂₉ N₅ O₇ S CJYMHKMECTVNSA-XLMAVXFVSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.13 Å
R-Value Free: 0.284 (Depositor), 0.270 (DCC)
R-Value Work: 0.240 (Depositor), 0.230 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.804	α = 90
b = 107.804	β = 90
c = 117.735	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
autoPROC	data scaling
MrBUMP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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

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.