7Q6P

Crystal Structure of bacterial Prolyl Peptidyl Isomerase with 5,5'-difluoroleucines

PDB DOI: https://doi.org/10.2210/pdb7Q6P/pdb

Classification: ISOMERASE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2021-11-09 Released: 2022-11-16
Deposition Author(s): Tars, K., Jaudzems, K., Recacha, R.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.239 (Depositor), 0.240 (DCC)
R-Value Observed:
0.241 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of bacterial Prolyl Peptidyl Isomerase with 5,5'-difluoroleucines

Tars, K., Jaudzems, K., Recacha, R.

To be published.

Macromolecule Content

Total Structure Weight: 77.02 kDa
Atom Count: 5,549
Modelled Residue Count: 641
Deposited Residue Count: 680
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase B	A, B, C, D	170	Escherichia coli K-12	Mutation(s): 0 Gene Names: ppiB, b0525, JW0514 EC: 5.2.1.8
UniProt
Find proteins for P23869 (Escherichia coli (strain K12)) Explore P23869 Go to UniProtKB: P23869
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23869
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain G [auth C]	E [auth A], F [auth B], G [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.239 (Depositor), 0.240 (DCC)
R-Value Observed: 0.241 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.061	α = 90
b = 83.46	β = 90
c = 122.84	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2022-11-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Not funded		--

Revision History (Full details and data files)

Version 1.0: 2022-11-16
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, 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.