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- PDB-5ylw: CYP76AH1 from Salvia miltiorrhiza -

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Basic information

Entry
Database: PDB / ID: 5ylw
TitleCYP76AH1 from Salvia miltiorrhiza
ComponentsFerruginol synthase
KeywordsOXIDOREDUCTASE / P450 / monoxygenase / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


ferruginol synthase / diterpenoid 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 / endoplasmic reticulum 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 / : / Ferruginol synthase
Similarity search - Component
Biological speciesSalvia miltiorrhiza (Chinese salvia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsChang, Z.
Funding support China, 1items
OrganizationGrant numberCountry
The National Natural Science Foundation of China81773833 China
CitationJournal: To Be Published
Title: CYP76AH1 from Salvia miltiorrhiza
Authors: Chang, Z.
History
DepositionOct 20, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ferruginol synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2653
Polymers55,5931
Non-polymers6712
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-17 kcal/mol
Surface area19840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.776, 108.776, 105.990
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Ferruginol synthase / Cytochrome P450 76AH1


Mass: 55593.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salvia miltiorrhiza (Chinese salvia) / Gene: CYP76AH1
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: S4UX02, EC: 1.14.13.190
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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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: 3.26 Å3/Da / Density % sol: 62.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion / Details: HEPES, Jeffamine M-600 Reagent, manganese chloride

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 79803 / % possible obs: 99.8 % / Redundancy: 6.5 % / Net I/σ(I): 24.15

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
MoRDaphasing
RefinementResolution: 1.7→48.389 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.565 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.16817 4021 5.1 %RANDOM
Rwork0.13734 ---
obs0.1389 75533 99.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.595 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.7→48.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3667 0 44 610 4321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.024040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9895530
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2325538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.14423.58176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.13815741
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.781530
X-RAY DIFFRACTIONr_chiral_restr0.0860.2607
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213083
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.04834040
X-RAY DIFFRACTIONr_sphericity_free33.38553
X-RAY DIFFRACTIONr_sphericity_bonded12.79554468
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 264 -
Rwork0.22 5219 -
obs--96.99 %

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