8HWP | pdb_00008hwp

Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 S12A in Complex with Butyrate

PDB DOI: https://doi.org/10.2210/pdb8HWP/pdb

Classification: HYDROLASE
Organism(s): Photobacterium sp. J15
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-01-02 Released: 2023-06-28
Deposition Author(s): Rahman, N.N.A., Leow, T.C., Jonet, M.A.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free:
0.275 (Depositor), 0.280 (DCC)
R-Value Work:
0.241 (Depositor), 0.250 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Mutant GDSL Esterase of Photobacterium sp. J15 in Complex with Butyrate

Rahman, N.N.A., Leow, T.C., Jonet, M.A.

To be published.

Macromolecule Content

Total Structure Weight: 35.73 kDa
Atom Count: 2,521
Modeled Residue Count: 328
Deposited Residue Count: 328
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDSL-family esterase	A	328	Photobacterium sp. J15	Mutation(s): 1
UniProt
Find proteins for A0A0K0PV22 (Photobacterium sp. J15(2011)) Explore A0A0K0PV22 Go to UniProtKB: A0A0K0PV22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A0K0PV22
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BUA (Subject of Investigation/LOI) Query on BUA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	butanoic acid C₄ H₈ O₂ FERIUCNNQQJTOY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.73 Å
R-Value Free: 0.275 (Depositor), 0.280 (DCC)
R-Value Work: 0.241 (Depositor), 0.250 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.007	α = 90
b = 56.626	β = 90
c = 119.678	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-06-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2023-06-28
Type: Initial release
Version 1.1: 2024-05-29
Changes: Data collection

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.