5D8M | pdb_00005d8m

Crystal structure of the metagenomic carboxyl esterase MGS0156

PDB DOI: https://doi.org/10.2210/pdb5D8M/pdb

Classification: HYDROLASE
Organism(s): uncultured organism
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-08-17 Released: 2016-10-05
Deposition Author(s): Cui, H., Nocek, B., Tchigvintsev, A., Popovic, A., Savchenko, A., Joachimiak, A., Yakunin, A.
Funding Organization(s): Genome Canada and Ontario Genomics Institute

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.190 (Depositor), 0.189 (DCC)
R-Value Work:
0.151 (Depositor), 0.152 (DCC)
R-Value Observed:
0.153 (Depositor)

wwPDB Validation 3D Report Full Report

Validation slider image for 5D8M

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of esterase (MGS0156)

Nocek, B., Cui, H., Tchigvintsev, A., Popovic, A., Savchenko, A., Joachimiak, A., Yakunin, A.

To be published.

Macromolecule Content

Total Structure Weight: 37.08 kDa
Atom Count: 2,793
Modeled Residue Count: 332
Deposited Residue Count: 347
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metagenomic carboxyl esterase MGS0156	A	347	uncultured organism	Mutation(s): 0
UniProt
Find proteins for A0A0G3FEJ8 (uncultured organism) Explore A0A0G3FEJ8 Go to UniProtKB: A0A0G3FEJ8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0G3FEJ8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	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: 0.190 (Depositor), 0.189 (DCC)
R-Value Work: 0.151 (Depositor), 0.152 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.764	α = 90
b = 95.907	β = 90
c = 135.604	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
SHELX	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2016-10-05

Deposition Author(s):

Tchigvintsev, A.

Funding Organization	Location	Grant Number
Genome Canada and Ontario Genomics Institute	Canada	BEEM project

Revision History (Full details and data files)

Version 1.0: 2016-10-05
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.