4OUK | pdb_00004ouk

Crystal structure of a C6-C4 SN3 inhibited ESTERASE B from LACTOBACILLUS RHAMNOSIS

PDB DOI: https://doi.org/10.2210/pdb4OUK/pdb

Classification: HYDROLASE
Organism(s): Lacticaseibacillus rhamnosus HN001
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2014-02-17 Released: 2014-08-27
Deposition Author(s): Colbert, D.A., Bennett, M.D., Lun, D.J., Holland, R., Delabre, M.-L., Loo, T.S., Anderson, B.F., Norris, G.E.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.229 (Depositor), 0.232 (DCC)
R-Value Work:
0.188 (Depositor), 0.197 (DCC)
R-Value Observed:
0.190 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structure of a C6-C4 SN3 inhibited ESTERASE B from LACTOBACILLUS RHAMNOSIS

Colbert, D.A., Bennett, M.D., Lun, D.J., Holland, R., Delabre, M.-L., Loo, T.S., Anderson, B.F., Norris, G.E.

To be published.

Macromolecule Content

Total Structure Weight: 36.19 kDa
Atom Count: 2,660
Modeled Residue Count: 309
Deposited Residue Count: 317
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Esterase B	A [auth X]	317	Lacticaseibacillus rhamnosus HN001	Mutation(s): 1 Gene Names: LRH_10360
UniProt
Find proteins for B2CZF4 (Lacticaseibacillus rhamnosus HN001) Explore B2CZF4 Go to UniProtKB: B2CZF4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B2CZF4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
C63 Query on C63 Download:Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	(2R)-2,3-bis(hexyloxy)propyl hydrogen (S)-pentylphosphonate C₂₀ H₄₃ O₅ P PSVODCVMDBUUJZ-HXUWFJFHSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.229 (Depositor), 0.232 (DCC)
R-Value Work: 0.188 (Depositor), 0.197 (DCC)
R-Value Observed: 0.190 (Depositor)

Space Group: I 4

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.077	α = 90
b = 110.077	β = 90
c = 59.375	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
MOLREP	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-27
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-20
Changes: 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.