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), 0.260 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

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

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

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
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), 0.260 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (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

Entry History 

Deposition Data

• Released Date: 2002-12-04 
Deposition Author(s): Jingzhi, L., Bingdong, S.

Revision History  

• 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