3I38 | pdb_00003i38

Structure of a putative chaperone protein dnaj from klebsiella pneumoniae subsp. pneumoniae mgh 78578

PDB DOI: https://doi.org/10.2210/pdb3I38/pdb

Classification: CHAPERONE
Organism(s): Klebsiella pneumoniae subsp. pneumoniae MGH 78578
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2009-06-30 Released: 2009-07-14
Deposition Author(s): Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Bearden, J., Joachimiak, A., Anderson, W.F., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.217 (Depositor), 0.228 (DCC)
R-Value Observed:
0.219 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3I38

This is version 1.3 of the entry. See complete history.

Literature

Structure of a Putative Chaperone Protein Dnaj from Klebsiella Pneumoniae Subsp. Pneumoniae Mgh 78578

Filippova, E.V., Minasov, G., Shuvalova, L., Kiryukhina, O., Bearden, J., Joachimiak, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 142.17 kDa
Atom Count: 9,501
Modeled Residue Count: 1,204
Deposited Residue Count: 1,308
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative chaperone DnaJ	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	109	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0 Gene Names: cbpA, KPN78578_44400, KPN_04509
UniProt
Find proteins for A6TH30 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TH30 Go to UniProtKB: A6TH30
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A6TH30
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, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.217 (Depositor), 0.228 (DCC)
R-Value Observed: 0.219 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.805	α = 81.75
b = 61.626	β = 78.71
c = 92.907	γ = 83.79

Software Package:

Software Name	Purpose
Blu-Ice	data collection
HKL-3000	phasing
MLPHARE	phasing
DM	model building
SHELXD	phasing
RESOLVE	model building
CCP4	model building
ARP/wARP	model building
Coot	model building
REFMAC	refinement
ADSC	data collection
HKL-2000	data scaling
DM	phasing
RESOLVE	phasing
ARP	model building
CCP4	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Filippova, E.V.

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Derived calculations, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.