3DPB | pdb_00003dpb

Crystal structure of the complex of the Caf1M chaperone with the mini-fiber of two Caf1 subunits (Caf1:Caf1), carrying the Ala9Val, Ala11Val, and Leu13Val mutations in the Gd donor strand

PDB DOI: https://doi.org/10.2210/pdb3DPB/pdb

Classification: CHAPERONE/STRUCTURAL PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-07-07 Released: 2009-07-14
Deposition Author(s): Fooks, L.J., Yu, X., Moslehi-Mohebi, E., Tischenko, V., Knight, S.D., MacIntyre, S., Zavialov, A.V.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.244 (Depositor), 0.240 (DCC)
R-Value Work:
0.198 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Hydrophobicity and rigidity of binding segments enable CAF1M chaperone to act as assembly catalyst

Fooks, L.J., Yu, X., Moslehi-Mohebi, E., Tischenko, V., Knight, S.D., MacIntyre, S., Zavialov, A.V.

To be published.

Macromolecule Content

Total Structure Weight: 57.56 kDa
Atom Count: 3,706
Modeled Residue Count: 473
Deposited Residue Count: 533
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chaperone protein caf1M	A	235	Yersinia pestis	Mutation(s): 0 Gene Names: caf1M, YPMT1.82, y5194, y1098, YP_pMT084
UniProt
Find proteins for P26926 (Yersinia pestis) Explore P26926 Go to UniProtKB: P26926
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26926
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
F1 capsule antigen	B, C	149	Yersinia pestis	Mutation(s): 3 Gene Names: caf1, YPMT1.84, y5196, y1100, YP_pMT082
UniProt
Find proteins for P26948 (Yersinia pestis) Explore P26948 Go to UniProtKB: P26948
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P26948
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.244 (Depositor), 0.240 (DCC)
R-Value Work: 0.198 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.909	α = 90
b = 179.955	β = 90
c = 45.62	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Moslehi-Mohebi, E.

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description
Version 1.4: 2024-11-20
Changes: 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.