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- PDB-7x2q: Salvia miltiorrhiza CYP76AH3 -

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Basic information

Entry
Database: PDB / ID: 7x2q
TitleSalvia miltiorrhiza CYP76AH3
ComponentsSugiol synthase
KeywordsOXIDOREDUCTASE / P450 protein / MEMBRANE PROTEIN
Function / homology
Function and homology information


ferruginol monooxygenase / sugiol synthase / terpenoid biosynthetic process / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / iron ion binding / heme binding / membrane
Similarity search - Function
Cytochrome P450, E-class, group I / 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 / Sugiol synthase
Similarity search - Component
Biological speciesSalvia miltiorrhiza (redroot sage)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.68 Å
AuthorsChang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: To Be Published
Title: Structure of CYP76AH3 at 3.67 Angstroms resolution
Authors: Chang, Z.
History
DepositionFeb 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sugiol synthase
B: Sugiol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5514
Polymers107,3182
Non-polymers1,2332
Water32418
1
A: Sugiol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2762
Polymers53,6591
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-17 kcal/mol
Surface area19620 Å2
MethodPISA
2
B: Sugiol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2762
Polymers53,6591
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-21 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.100, 151.100, 156.910
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Space group name HallP6c2c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z+1/2
#9: y,x,-z
#10: -y,-x,-z+1/2
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/2

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Components

#1: Protein Sugiol synthase / Cytochrome P450 76AH3 / Ferruginol monooxygenase


Mass: 53659.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia miltiorrhiza (redroot sage) / Gene: CYP76AH3 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0Y0GRS3, sugiol synthase, ferruginol monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 289.1 K / Method: vapor diffusion / Details: 1600mmol/L sodium citrate tribasic

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Data collection

DiffractionMean temperature: 193.1 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.97853 Å
DetectorType: Brandeis B4 / Detector: CCD / Date: May 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.67→39.23 Å / Num. obs: 11668 / % possible obs: 96.8 % / Redundancy: 35.5 % / Biso Wilson estimate: 67.16 Å2 / Rpim(I) all: 0.064 / Net I/σ(I): 16.5
Reflection shellResolution: 3.67→4.04 Å / Num. unique obs: 11620 / CC1/2: 0.741
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 3.68→39.23 Å / SU ML: 0.4803 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.9293
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2963 562 4.84 %
Rwork0.2514 11058 -
obs0.2538 11620 96.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.99 Å2
Refinement stepCycle: LAST / Resolution: 3.68→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7488 0 0 18 7506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337678
X-RAY DIFFRACTIONf_angle_d0.632610418
X-RAY DIFFRACTIONf_chiral_restr0.04341126
X-RAY DIFFRACTIONf_plane_restr0.00491344
X-RAY DIFFRACTIONf_dihedral_angle_d18.04262902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.68-4.040.39351170.28352697X-RAY DIFFRACTION96.21
4.04-4.630.30261290.24632710X-RAY DIFFRACTION96.43
4.63-5.830.30561580.24652729X-RAY DIFFRACTION96.52
5.83-39.230.25171580.23922922X-RAY DIFFRACTION97.13

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