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- PDB-9ln5: Crystal structure of P450revI A241L mutant in complex with revero... -

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Basic information

Entry
Database: PDB / ID: 9ln5
TitleCrystal structure of P450revI A241L mutant in complex with reveromycin T
ComponentsPutative monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Heme / Reveromycin / Biosynthesis
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding
Similarity search - Function
Cytochrome P450, B-class / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-RRM / Putative monooxygenase
Similarity search - Component
Biological speciesStreptomyces sp. SN-593 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsFujiyama, K. / Yong, Y.F. / Takahashi, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H00416 Japan
CitationJournal: Chem Sci / Year: 2025
Title: Biosynthesis of reveromycin derivatives by altering the regioselectivity of cytochrome P450revI
Authors: Yong, Y.F. / Liu, S. / Sakai, K. / Fujiyama, K. / Takagi, H. / Futamura, Y. / Shimizu, T. / Osada, H. / Ong, E.B.B. / Takahashi, S.
History
DepositionJan 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0265
Polymers44,7941
Non-polymers1,2324
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-25 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.791, 72.791, 348.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-720-

HOH

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Components

#1: Protein Putative monooxygenase / Reveromycin T hydroxylase


Mass: 44794.074 Da / Num. of mol.: 1 / Mutation: A241L
Source method: isolated from a genetically manipulated source
Details: The initial 'GSH' is residual amino acid from thrombin recognition site.
Source: (gene. exp.) Streptomyces sp. SN-593 (bacteria) / Gene: revI, RVR_8636 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G1UDU7
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-RRM / (2E,4S,5S,6E,8E)-10-{(2R,3S,6S,8R,9S)-9-butyl-8-[(1E,3E)-4-carboxy-3-methylbuta-1,3-dien-1-yl]-3-methyl-1,7-dioxaspiro[5.5]undec-2-yl}-5-hydroxy-4,8-dimethyldeca-2,6,8-trienoic acid


Mass: 544.719 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C32H48O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.97 Å3/Da / Density % sol: 58.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1.0M Sodium citrate, 0.2M Sodium chloride, 0.1M Tris (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.025 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.025 Å / Relative weight: 1
ReflectionResolution: 2.13→42.707122167 Å / Num. obs: 31933 / % possible obs: 99.96 % / Redundancy: 37.6 % / Biso Wilson estimate: 41.3171336863 Å2 / CC1/2: 0.999 / Net I/σ(I): 25.01
Reflection shellResolution: 2.13→2.206 Å / Mean I/σ(I) obs: 3.51 / Num. unique obs: 3118 / CC1/2: 0.936

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Processing

Software
NameVersionClassification
XDSVERSION Jun 30, 2023 BUILT=20230630data reduction
XDSVERSION Jun 30, 2023 BUILT=20230630data scaling
pointless1.12.15data scaling
Aimless0.7.13data scaling
PHASER2.8.3phasing
Coot0.9.8.92model building
REFMAC5.8.0419refinement
PHENIX1.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→42.707 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2736 1574 4.93 %
Rwork0.229 --
obs0.2313 31930 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.13→42.707 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3100 0 84 150 3334
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033321
X-RAY DIFFRACTIONf_angle_d0.584533
X-RAY DIFFRACTIONf_dihedral_angle_d14.0242020
X-RAY DIFFRACTIONf_chiral_restr0.038489
X-RAY DIFFRACTIONf_plane_restr0.004603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.19880.40221430.34722669X-RAY DIFFRACTION100
2.1988-2.27740.36151460.33342697X-RAY DIFFRACTION100
2.2774-2.36860.35651250.32232687X-RAY DIFFRACTION100
2.3686-2.47630.34531450.30222684X-RAY DIFFRACTION100
2.4763-2.60690.35031300.30792730X-RAY DIFFRACTION100
2.6069-2.77020.35881310.29882715X-RAY DIFFRACTION100
2.7702-2.9840.34771310.27362739X-RAY DIFFRACTION100
2.984-3.28420.30911500.24682760X-RAY DIFFRACTION100
3.2842-3.75920.24141560.2082765X-RAY DIFFRACTION100
3.7592-4.73520.20541670.1712830X-RAY DIFFRACTION100
4.7352-42.7070.24271500.1843080X-RAY DIFFRACTION100

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