3GRH

Crystal structure of escherichia coli ybhc

• PDB DOI: https://doi.org/10.2210/pdb3GRH/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-25 Released: 2009-04-07 
• Deposition Author(s): Eklof, J.M., Tan, T.C., Divne, C., Brumer, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Literature

The crystal structure of the outer membrane lipoprotein YbhC from Escherichia coli sheds new light on the phylogeny of carbohydrate esterase family 8.

Eklof, J.M., Tan, T.C., Divne, C., Brumer, H.

(2009) Proteins 76: 1029-1036

• PubMed: 19452549 
• DOI: https://doi.org/10.1002/prot.22453
• Primary Citation of Related Structures:  
  3GRH

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Organizational Affiliation: 

School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, S 106 91 Stockholm, Sweden.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 45.96 kDa 
• Atom Count: 3,287 
• Modelled Residue Count: 397 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acyl-CoA thioester hydrolase ybgC	A	422	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0772, JW0755, ybhC EC: 3.1.2
UniProt
Find proteins for P46130 (Escherichia coli (strain K12)) Explore P46130  Go to UniProtKB:  P46130

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.2	α = 90
b = 79.2	β = 90
c = 159.65	γ = 120

Software Package:

Software Name	Purpose
ProDC	data collection
SHELXS	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Eklof, J.M., Tan, T.C., Divne, C., Brumer, H.

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2018-05-23
  Changes: Data collection
• Version 1.3: 2019-12-11
  Changes: Data collection, Database references
• Version 1.4: 2024-11-13
  Changes: Data collection, Database references, Structure summary