3GRH | pdb_00003grh

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.208 (Depositor), 0.212 (DCC)
R-Value Work:
0.193 (Depositor), 0.198 (DCC)
R-Value Observed:
0.193 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 3GRH

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

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 Search on PubMed
DOI: https://doi.org/10.1002/prot.22453
Primary Citation Related Structures:
3GRH

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46130
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.208 (Depositor), 0.212 (DCC)
R-Value Work: 0.193 (Depositor), 0.198 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Revision History (Full details and data files)

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

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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.