3DKR | pdb_00003dkr

Snapshots of esterase D from lactobacillus rhamnosus: Insights into a rotation driven catalytic mechanism

PDB DOI: https://doi.org/10.2210/pdb3DKR/pdb

Classification: HYDROLASE
Organism(s): Lacticaseibacillus rhamnosus HN001
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2008-06-25 Released: 2009-06-30
Deposition Author(s): Bennett, M.D., Delabre, M.-L., Holland, R., Norris, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.184 (Depositor), 0.186 (DCC)
R-Value Work:
0.167 (Depositor), 0.169 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of esterase D from lactobacillus rhamnosus

Bennett, M.D., Delabre, M.-L., Holland, R., Norris, G.E.

To be published.

Macromolecule Content

Total Structure Weight: 27.45 kDa
Atom Count: 2,102
Modeled Residue Count: 241
Deposited Residue Count: 251
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase D	A	251	Lacticaseibacillus rhamnosus HN001	Mutation(s): 0 Gene Names: EstD
UniProt
Find proteins for B2CZF3 (Lacticaseibacillus rhamnosus HN001) Explore B2CZF3 Go to UniProtKB: B2CZF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2CZF3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] mmCIF format, chain B [auth A] mmCIF format, chain C [auth A]	B [auth A], C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.184 (Depositor), 0.186 (DCC)
R-Value Work: 0.167 (Depositor), 0.169 (DCC)
R-Value Observed: 0.167 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.225	α = 90
b = 47.225	β = 90
c = 174.572	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data scaling
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-06-30

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-06-30
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, 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.