9IQI | pdb_00009iqi

Structure of oleate hydratase mutant - V135A/L212V from Staphylococcus aureus in the complex with FAD

PDB DOI: https://doi.org/10.2210/pdb9IQI/pdb

Classification: LYASE
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-07-12 Released: 2025-07-16
Deposition Author(s): Xue, S., Feng, T.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.235 (Depositor), 0.235 (DCC)
R-Value Work:
0.201 (Depositor), 0.202 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Cooperative Evolution of Oleate Hydratase via Combinatorial Distal Site Mutations

Xue, S., Feng, T.

To be published.

Macromolecule Content

Total Structure Weight: 205.02 kDa
Atom Count: 14,557
Modeled Residue Count: 1,761
Deposited Residue Count: 1,776
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oleate hydratase	A, B, C	592	Staphylococcus aureus	Mutation(s): 2 Gene Names: EP54_06595, EQ90_12415, GO814_02765, GO942_14045, GZ163_10760, HMPREF3211_02399 EC: 4.2.1.53
UniProt
Find proteins for Q2G1P3 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2G1P3 Go to UniProtKB: Q2G1P3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2G1P3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth C] mmCIF format, chain D [auth A] mmCIF format, chain E [auth C]	D [auth A], E [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain D [auth A] Focus chain E [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.235 (Depositor), 0.235 (DCC)
R-Value Work: 0.201 (Depositor), 0.202 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 188.476	α = 90
b = 109.809	β = 116.61
c = 118.322	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-07-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government	China	2021YFC2103702

Revision History (Full details and data files)

Version 1.0: 2025-07-16
Type: Initial release

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.