1KHY | pdb_00001khy

The Crystal Structure of ClpB N Terminal Domain, Implication to the Peptide Binding Function of ClpB

PDB DOI: https://doi.org/10.2210/pdb1KHY/pdb

Classification: CHAPERONE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2001-12-01 Released: 2002-12-04
Deposition Author(s): Jingzhi, L., Bingdong, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.259 (Depositor), 0.259 (DCC)
R-Value Work:
0.222 (Depositor), 0.222 (DCC)
R-Value Observed:
0.226 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of E. coli Hsp100 ClpB N Terminal Domain, Implication to Peptide Binding Function of ClpB

Jingzhi, L., Bingdong, S.

To be published.

Macromolecule Content

Total Structure Weight: 63.68 kDa
Atom Count: 4,304
Modeled Residue Count: 540
Deposited Residue Count: 592
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CLPB PROTEIN	A, B, C, D	148	Escherichia coli	Mutation(s): 3 Gene Names: clpb
UniProt
Find proteins for P63284 (Escherichia coli (strain K12)) Explore P63284 Go to UniProtKB: P63284
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63284
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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.259 (Depositor), 0.259 (DCC)
R-Value Work: 0.222 (Depositor), 0.222 (DCC)
R-Value Observed: 0.226 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.213	α = 90.45
b = 52.6	β = 111.73
c = 56.841	γ = 107.05

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2002-12-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-12-04
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2021-07-21
Changes: Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, 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.