8YRB | pdb_00008yrb

Structure of cyclohexanone monooxygenase mutant from Acinetobacter calcoaceticus

PDB DOI: https://doi.org/10.2210/pdb8YRB/pdb

Classification: OXIDOREDUCTASE
Organism(s): Acinetobacter calcoaceticus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2024-03-21 Released: 2025-04-02
Deposition Author(s): Qiang, G., Zheng, Y.C., Feng, L., Yu, H.L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free:
0.227 (Depositor), 0.225 (DCC)
R-Value Work:
0.187 (Depositor), 0.185 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: in silico
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Ligand Structure Quality Assessment

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

Literature

Loop Engineering Facilitates the Nicotinamide Cofactors Utilization of BVMOs

Qiang, G., Zheng, Y.C., Feng, L., Yu, H.L.

To be published.

Macromolecule Content

Total Structure Weight: 63.56 kDa
Atom Count: 4,588
Modeled Residue Count: 515
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative flavin-binding monooxygenase	A	548	Acinetobacter calcoaceticus	Mutation(s): 19 Gene Names: P23_1101

Small Molecules

Ligands 2 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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NDP (Subject of Investigation/LOI) Query on NDP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.78 Å
R-Value Free: 0.227 (Depositor), 0.225 (DCC)
R-Value Work: 0.187 (Depositor), 0.185 (DCC)
R-Value Observed: 0.189 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.02	α = 90
b = 53.22	β = 96.485
c = 100.81	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2025-04-02

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	21922804

Revision History (Full details and data files)

Version 1.0: 2025-04-02
Type: Initial release

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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.