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- PDB-7v50: Structure of cyclohexanone monooxygenase mutant from Acinetobacte... -

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Basic information

Entry
Database: PDB / ID: 7v50
TitleStructure of cyclohexanone monooxygenase mutant from Acinetobacter calcoaceticus
ComponentsPutative flavin-binding monooxygenase
KeywordsOXIDOREDUCTASE / BVMO_positive mutant
Function / homologyFlavin monooxygenase-like / Flavin-binding monooxygenase-like / N,N-dimethylaniline monooxygenase activity / FAD/NAD(P)-binding domain superfamily / NADP binding / flavin adenine dinucleotide binding / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Putative flavin-binding monooxygenase
Function and homology information
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 2.0Apr 12, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_peptide_omega / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_asym / struct_conf / struct_mon_prot_cis / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
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_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_entry_details.has_ligand_of_interest / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _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 / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Description: Ligand identity
Details: The NADP+ was mis-refined into a wrong position. Besides, residue 485-500 was refined.
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_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _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)64,8603
Polymers63,3311
Non-polymers1,5292
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area22620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.305, 52.900, 102.994
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative flavin-binding monooxygenase


Mass: 63330.574 Da / Num. of mol.: 1
Mutation: F246Y,F277L,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.: 213 / 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: 2.36 Å3/Da / Density % sol: 47.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: bicine/Trizma base, PEG20000, PEG MME 550, 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 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.07→50 Å / Num. obs: 34734 / % possible obs: 99.9 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 33.75
Reflection shellResolution: 2.08→2.12 Å / Rmerge(I) obs: 0.07 / Num. unique obs: 34734

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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: 2.3→38.87 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 1273 4.97 %
Rwork0.211 --
obs0.2131 25600 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 101 213 4388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024274
X-RAY DIFFRACTIONf_angle_d0.5775804
X-RAY DIFFRACTIONf_dihedral_angle_d12.161586
X-RAY DIFFRACTIONf_chiral_restr0.043627
X-RAY DIFFRACTIONf_plane_restr0.004732
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.34271160.27262653X-RAY DIFFRACTION98
2.39-2.50.30661370.25182680X-RAY DIFFRACTION100
2.5-2.630.31691540.24742683X-RAY DIFFRACTION100
2.63-2.80.32171360.23912695X-RAY DIFFRACTION100
2.8-3.010.30521390.23972680X-RAY DIFFRACTION100
3.01-3.320.25521470.22812717X-RAY DIFFRACTION100
3.32-3.80.24841540.20222703X-RAY DIFFRACTION100
3.8-4.780.2121460.16582717X-RAY DIFFRACTION100
4.78-38.870.18031440.18162799X-RAY DIFFRACTION100

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