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- PDB-7v4x: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 7v4x
TitleStructure of cyclohexanone monooxygenase mutant from Acinetobacter calcoaceticus
ComponentsPutative flavin-binding monooxygenase
KeywordsOXIDOREDUCTASE / BVMO
Function / homology
Function and homology information


N,N-dimethylaniline monooxygenase activity / NADP binding / flavin adenine dinucleotide binding
Similarity search - Function
: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative flavin-binding monooxygenase
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å
AuthorsWu, Y. / Yu, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: CHINESE J CATAL / Year: 2023
Title: Precise regulation of the substrate selectivity of Baeyer-Villiger monooxygenase to minimize overoxidation of prazole sulfoxides.
Authors: Wu, Y. / Chen, Q.Q. / Chen, Q. / Geng, Q. / Zhang, Q. / Zheng, Y.C. / Zhao, C. / Zhang, Y. / Zhou, J. / Wang, B. / Xu, J.H. / Yu, H.L.
History
DepositionAug 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 2.0Jul 12, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_poly / entity_poly_seq / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_conf / struct_mon_prot_cis / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_poly_seq.mon_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_ligand_of_interest / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.d_res_high / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length
Description: Model completeness
Details: We refined the position of NADP+, besides, the missing residues from 490 to 500 were modelled according to the electron density.
Provider: author / Type: Coordinate replacement
Revision 2.1Sep 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 2.2Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)62,7213
Polymers61,1921
Non-polymers1,5292
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-9 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.595, 52.999, 100.489
Angle α, β, γ (deg.)90.00, 96.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative flavin-binding monooxygenase / cyclohexanone monooxygenase


Mass: 61192.168 Da / Num. of mol.: 1
Mutation: F246Y,K326C,N386S,I388K,M390I,L426F,F432L,T433A,L435S,S438I,E488K,S489C,W490R,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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: bicine/Trizma base, PEG1000, PEG3350, MPD, and 1,6-Hexanediol, 1-Butanal, 1,2-Propanediol, 1,4-Butanediol, 1,3-Propanediol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.33→46.81 Å / Num. obs: 23565 / % possible obs: 99.7 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 12.6
Reflection shellResolution: 2.34→2.38 Å / Rmerge(I) obs: 0.17 / Num. unique obs: 664779 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6A37

6a37


Resolution: 2.33→46.81 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2354 1101 5.13 %
Rwork0.1867 --
obs0.1892 21447 90.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.33→46.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4204 0 101 163 4468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034408
X-RAY DIFFRACTIONf_angle_d0.665984
X-RAY DIFFRACTIONf_dihedral_angle_d11.948605
X-RAY DIFFRACTIONf_chiral_restr0.044644
X-RAY DIFFRACTIONf_plane_restr0.004757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.33-2.440.2889600.25531357X-RAY DIFFRACTION48
2.44-2.570.32441120.23842246X-RAY DIFFRACTION80
2.57-2.730.30771410.22682692X-RAY DIFFRACTION97
2.73-2.940.29471290.2212815X-RAY DIFFRACTION99
2.94-3.240.25351590.20682773X-RAY DIFFRACTION100
3.24-3.710.23011460.17942804X-RAY DIFFRACTION100
3.71-4.670.18641720.15272798X-RAY DIFFRACTION100
4.67-46.810.21441820.16492861X-RAY DIFFRACTION100

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