3KOP | pdb_00003kop

Crystal structure of Protein with a cyclophilin-like fold (YP_831253.1) from Arthrobacter sp. FB24 at 1.90 A resolution

PDB DOI: https://doi.org/10.2210/pdb3KOP/pdb

Classification: Structural Genomics, Unknown function
Organism(s): Arthrobacter sp. FB24
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-11-13 Released: 2009-11-24
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.196 (Depositor), 0.199 (DCC)
R-Value Work:
0.160 (Depositor), 0.167 (DCC)
R-Value Observed:
0.162 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of Protein with a cyclophilin-like fold (YP_831253.1) from Arthrobacter sp. FB24 at 1.90 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 125.66 kDa
Atom Count: 8,455
Modeled Residue Count: 971
Deposited Residue Count: 1,128
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B, C, D, E A, B, C, D, E, F	188	Arthrobacter sp. FB24	Mutation(s): 0 Gene Names: Arth_1761
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.196 (Depositor), 0.199 (DCC)
R-Value Work: 0.160 (Depositor), 0.167 (DCC)
R-Value Observed: 0.162 (Depositor)

Diffraction Data: https://doi.org/10.18430/M33KOP

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.294	α = 90
b = 98.102	β = 93.19
c = 84.503	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-11-24

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-11-24
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Source and taxonomy, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2019-07-17
Changes: Advisory, Data collection, Derived calculations, Refinement description
Version 1.4: 2024-11-20
Changes: Data collection, Database references, Structure summary

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.