5XB0 | pdb_00005xb0

1.6 A crystal structure of peptidyl-prolyl cis-trans isomerase PPIase from Pseudomonas syringae pv. tomato str. DC3000 (PSPTO DC3000)

PDB DOI: https://doi.org/10.2210/pdb5XB0/pdb
Entry: 5XB0 supersedes: 3OE2

Classification: ISOMERASE
Organism(s): Pseudomonas syringae pv. tomato str. DC3000
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-03-15 Released: 2017-04-19
Deposition Author(s): Zhang, H., Gao, Y., Li, M., Chang, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.198 (Depositor), 0.200 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (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

1.6 A crystal structure of peptidyl-prolyl cis-trans isomerase PPIase from Pseudomonas syringae pv. tomato str. DC3000 (PSPTO DC3000)

Zhang, H., Gao, Y., Li, M., Chang, W.

To be published.

Macromolecule Content

Total Structure Weight: 14.45 kDa
Atom Count: 1,197
Modeled Residue Count: 133
Deposited Residue Count: 133
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase	A	133	Pseudomonas syringae pv. tomato str. DC3000	Mutation(s): 0 Gene Names: PSPTO_0135 EC: 5.2.1.8
UniProt
Find proteins for Q88B84 (Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000)) Explore Q88B84 Go to UniProtKB: Q88B84
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q88B84
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TLA Query on TLA 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]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.198 (Depositor), 0.200 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.222	α = 90
b = 44.099	β = 90
c = 82.312	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2017-04-19

Deposition Author(s):

This entry supersedes: 3OE2

Revision History (Full details and data files)

Version 1.0: 2017-04-19
Type: Initial release
Version 1.1: 2023-11-22
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.