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- PDB-6a37: X-ray structure of cyclohexanone monooxygenase from Acinetobacter... -

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Basic information

Entry
Database: PDB / ID: 6a37
TitleX-ray structure of cyclohexanone monooxygenase from Acinetobacter calcoaceticus
ComponentsPutative flavin-binding monooxygenase
KeywordsOXIDOREDUCTASE / cyclohexanone monooxygenase / FAD binding
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / flavin adenine dinucleotide binding / NADP binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsZhang, Y. / Yu, H.L. / Xu, J.H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China21536004 China
National Natural Science Foundation of China21672063 China
National Natural Science Foundation of China21776085 China
CitationJournal: Acs Sustain Chem Eng
Title: Engineering of Cyclohexanone Monooxygenase for the Enantioselective Synthesis of (S)-Omeprazole
Authors: Zhang, Y. / Wu, Y.Q. / Xu, N. / Zhao, Q. / Yu, H.L. / Xu, J.H.
History
DepositionJun 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative flavin-binding monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0902
Polymers62,3041
Non-polymers7861
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.100, 52.969, 102.162
Angle α, β, γ (deg.)90.00, 96.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative flavin-binding monooxygenase


Mass: 62304.234 Da / Num. of mol.: 1
Mutation: F246Y, K326C, L426F, F432L, T433A, L435S, S438I, F505L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: P23_1101
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0A8XFY0
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.19 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (w/v) PEG 3350, 0.1 M Tris-HCl (pH 8.5), 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 28080 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.157 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.464

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UCL

3ucl


Resolution: 2.204→48.386 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.7
RfactorNum. reflection% reflection
Rfree0.2293 1409 5.02 %
Rwork0.1846 --
obs0.1868 28063 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.204→48.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 0 53 238 4353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074211
X-RAY DIFFRACTIONf_angle_d1.0935712
X-RAY DIFFRACTIONf_dihedral_angle_d15.3921532
X-RAY DIFFRACTIONf_chiral_restr0.074616
X-RAY DIFFRACTIONf_plane_restr0.004730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2043-2.28310.2291350.19882508X-RAY DIFFRACTION95
2.2831-2.37450.27331410.21312670X-RAY DIFFRACTION100
2.3745-2.48250.27611260.21132687X-RAY DIFFRACTION100
2.4825-2.61340.26461320.212660X-RAY DIFFRACTION100
2.6134-2.77710.28581490.20952651X-RAY DIFFRACTION100
2.7771-2.99150.24981310.21112677X-RAY DIFFRACTION100
2.9915-3.29250.23091610.20732656X-RAY DIFFRACTION100
3.2925-3.76880.24191410.17672701X-RAY DIFFRACTION100
3.7688-4.74760.18921490.15722683X-RAY DIFFRACTION100
4.7476-48.3980.21271440.17312761X-RAY DIFFRACTION100

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