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- PDB-7wzm: Crystal structure of Cytochrome P450 184A1 from streptomyces aver... -

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Basic information

Entry
Database: PDB / ID: 7wzm
TitleCrystal structure of Cytochrome P450 184A1 from streptomyces avermitilis in complex with Oleic acid
ComponentsPutative cytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Streptomyces avermitilis / Oleic acid
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, 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 / OLEIC ACID / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsKim, V.C. / Kim, D.G. / Lee, S.G. / Lee, G.H. / Lee, S.A. / Kang, L.W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of Cytochrome P450 184A1 from streptomyces avermitilis in complex with Oleic acid
Authors: Kim, V.C. / Kim, D.G. / Lee, S.G. / Lee, G.H. / Lee, S.A. / Kang, L.W.
History
DepositionFeb 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6703
Polymers53,7711
Non-polymers8992
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-24 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.687, 62.652, 132.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative cytochrome P450


Mass: 53770.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria)
Strain: ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680
Gene: cyp21, SAVERM_5111 / Production host: Escherichia coli (E. coli) / References: UniProt: Q82D73
#2: Chemical ChemComp-OLA / OLEIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 288.15 K / Method: vapor diffusion, sitting drop
Details: 15% PEG3350, 0.2 M sodium chloride, 0.1M HEPES, pH 7.0, 5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. obs: 52789 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 0.949 / Net I/σ(I): 36.567
Reflection shellResolution: 1.68→1.71 Å / Num. unique obs: 52789 / CC1/2: 0.889

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7WZL

7wzl


Resolution: 1.68→45.52 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.796 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2619 5 %RANDOM
Rwork0.1879 ---
obs0.1895 50100 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69 Å2 / Biso mean: 14.682 Å2 / Biso min: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0 Å2-0 Å2
2---0.28 Å20 Å2
3---0.43 Å2
Refinement stepCycle: final / Resolution: 1.68→45.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3469 0 63 178 3710
Biso mean--18.55 22.05 -
Num. residues----458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133620
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173427
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.6774934
X-RAY DIFFRACTIONr_angle_other_deg1.5731.67826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.8119.417206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63915530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0841544
X-RAY DIFFRACTIONr_chiral_restr0.0940.2450
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024179
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02887
LS refinement shellResolution: 1.68→1.722 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.234 182 -
Rwork0.186 3626 -
obs--98.91 %

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