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- PDB-9orn: Structure of the Acinetobacter calcoaceticus Cyclohexanone Monoox... -

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Basic information

Entry
Database: PDB / ID: 9orn
TitleStructure of the Acinetobacter calcoaceticus Cyclohexanone Monooxygenase mutant M10-R327K-R490E-I491E-Y246F-S186W-T187V
ComponentsPutative flavin-binding monooxygenase
KeywordsOXIDOREDUCTASE / CYCLOHEXANONE MONOOXYGENASE / FAD BINDING / Acinetobacter calcoaceticus
Function / homology: / Flavin monooxygenase-like / Flavin-binding monooxygenase-like / N,N-dimethylaniline monooxygenase activity / FAD/NAD(P)-binding domain superfamily / flavin adenine dinucleotide binding / NADP binding / FLAVIN-ADENINE DINUCLEOTIDE / Putative flavin-binding monooxygenase
Function and homology information
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRaps, F.C. / Jeffrey, P.D. / Sorigue, D. / Hyster, T.K.
Funding support United States, Switzerland, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127703 United States
Swiss National Science FoundationP500PN 202708 Switzerland
CitationJournal: To Be Published
Title: Stereoselective Photoenzymatic Hydroarylations Forming Quaternary Stereocenters
Authors: Raps, F.C. / Chufan, J. / Brown, A.C. / Sorigue, D. / Hyster, T.K.
History
DepositionMay 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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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)62,1022
Polymers61,3161
Non-polymers7861
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.349, 53.487, 101.494
Angle α, β, γ (deg.)90.000, 99.894, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Putative flavin-binding monooxygenase


Mass: 61316.160 Da / Num. of mol.: 1 / Mutation: M10-R327K-R490E-I491E-Y246F-S186W-T187V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Gene: P23_1101 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A8XFY0
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris pH8, NaCl, PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.75→28.37 Å / Num. obs: 57097 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 23.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.033 / Rrim(I) all: 0.088 / Χ2: 0.97 / Net I/σ(I): 15 / Num. measured all: 393366
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 100 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.912 / Num. measured all: 21596 / Num. unique obs: 3134 / CC1/2: 0.541 / Rpim(I) all: 0.373 / Rrim(I) all: 0.987 / Χ2: 0.74 / Net I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→28.37 Å / SU ML: 0.2229 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.2645
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2103 2801 4.91 %
Rwork0.1773 54280 -
obs0.1789 57081 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.97 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 53 466 4688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664384
X-RAY DIFFRACTIONf_angle_d0.81885962
X-RAY DIFFRACTIONf_chiral_restr0.0551645
X-RAY DIFFRACTIONf_plane_restr0.0052764
X-RAY DIFFRACTIONf_dihedral_angle_d21.24491605
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.780.31621350.28372731X-RAY DIFFRACTION100
1.78-1.810.31441460.27242625X-RAY DIFFRACTION100
1.81-1.850.2781330.25422749X-RAY DIFFRACTION100
1.85-1.890.29851280.23532691X-RAY DIFFRACTION100
1.89-1.930.27271530.22892675X-RAY DIFFRACTION100
1.93-1.970.23371420.20352693X-RAY DIFFRACTION99.96
1.97-2.020.2081460.18772686X-RAY DIFFRACTION99.96
2.02-2.070.23771420.19772698X-RAY DIFFRACTION99.96
2.07-2.140.23821190.19012764X-RAY DIFFRACTION100
2.14-2.20.21621390.18622670X-RAY DIFFRACTION100
2.2-2.280.23731490.18462688X-RAY DIFFRACTION99.89
2.28-2.370.21471390.1822704X-RAY DIFFRACTION100
2.37-2.480.22161480.1772696X-RAY DIFFRACTION100
2.48-2.610.21421380.182721X-RAY DIFFRACTION100
2.61-2.780.22951450.19012723X-RAY DIFFRACTION100
2.78-2.990.24681430.18332730X-RAY DIFFRACTION100
2.99-3.290.21651660.18052703X-RAY DIFFRACTION99.97
3.29-3.770.16981290.15872733X-RAY DIFFRACTION99.9
3.77-4.740.17281240.13732774X-RAY DIFFRACTION99.93
4.74-28.370.16041370.15812826X-RAY DIFFRACTION99.8

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