4XVV | pdb_00004xvv

Crystal structure of an Acid stress chaperone HdeB (KPN_03484) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution

• PDB DOI: https://doi.org/10.2210/pdb4XVV/pdb

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


• Deposited: 2015-01-28 Released: 2015-02-11 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.226 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Literature

Crystal structure of an Acid stress chaperone HdeB (KPN_03484) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 17.81 kDa 
• Atom Count: 1,302 
• Modeled Residue Count: 150 
• Deposited Residue Count: 154 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acid stress chaperone HdeB	A, B	77	Klebsiella pneumoniae subsp. pneumoniae MGH 78578	Mutation(s): 0  Gene Names: hdeB, KPN_03484
UniProt
Find proteins for A6TE95 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)) Explore A6TE95  Go to UniProtKB:  A6TE95

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.226 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m30c7c

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.475	α = 90
b = 39.443	β = 90
c = 98.256	γ = 90

Software Package:

Software Name	Purpose
PDB_EXTRACT	data extraction
SOLVE	phasing
XSCALE	data scaling
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-02-11 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	U54 GM094586

Revision History  

• Version 1.0: 2015-02-11
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2023-02-01
  Changes: Data collection, Database references
• Version 1.5: 2024-11-13
  Changes: Data collection, Structure summary