7E16 | pdb_00007e16

crystal structure of GDSL esterase from Geobacillus thermodenitrificans

PDB DOI: https://doi.org/10.2210/pdb7E16/pdb

Classification: HYDROLASE
Organism(s): Geobacillus thermodenitrificans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-01-31 Released: 2021-04-14
Deposition Author(s): Chen, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free:
0.278 (Depositor), 0.272 (DCC)
R-Value Work:
0.245 (Depositor), 0.243 (DCC)
R-Value Observed:
0.246 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7E16

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

Literature

Rational engineering of substrate selectivity of GDSL esterase from Geobacillus thermodenitrificans

Zhang, Y.

To be published.

Macromolecule Content

Total Structure Weight: 58.7 kDa
Atom Count: 3,262
Modeled Residue Count: 414
Deposited Residue Count: 526
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL-family esterase	A, B	263	Geobacillus thermodenitrificans	Mutation(s): 0
UniProt
Find proteins for B2ZAB3 (Geobacillus thermodenitrificans) Explore B2ZAB3 Go to UniProtKB: B2ZAB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2ZAB3
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.62 Å
R-Value Free: 0.278 (Depositor), 0.272 (DCC)
R-Value Work: 0.245 (Depositor), 0.243 (DCC)
R-Value Observed: 0.246 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.424	α = 90
b = 106.424	β = 90
c = 128.643	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2021-04-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2021-04-14
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Database references, Refinement description

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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.