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

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Basic information

Entry
Database: PDB / ID: 7wzl
TitleCrystal structure of Cytochrome P450 184A1 from streptomyces avermitilis
ComponentsPutative cytochrome P450
KeywordsOXIDOREDUCTASE / Cytochrome P450 / Streptomyces avermitilis
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 / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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
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

Downloads & links

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Assembly

Deposited unit
A: Putative cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3872
Polymers53,7711
Non-polymers6161
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-25 kcal/mol
Surface area18080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.668, 62.071, 134.296
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-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
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: 2.16 Å3/Da / Density % sol: 42.99 %
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: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 21998 / % possible obs: 99.2 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.111 / Net I/σ(I): 56.434
Reflection shellResolution: 2.27→2.31 Å / Rmerge(I) obs: 0.491 / Mean I/σ(I) obs: 7.883 / Num. unique obs: 21998 / CC1/2: 0.937

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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: 6L8I

6l8i


Resolution: 2.27→35.29 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 6.549 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.274 / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1049 4.8 %RANDOM
Rwork0.2041 ---
obs0.2064 20873 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.31 Å2 / Biso mean: 45.141 Å2 / Biso min: 24.53 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0 Å2-0 Å2
2---0.61 Å20 Å2
3---0.95 Å2
Refinement stepCycle: final / Resolution: 2.27→35.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3441 0 43 0 3484
Biso mean--31.49 --
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133574
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173395
X-RAY DIFFRACTIONr_angle_refined_deg1.551.6744872
X-RAY DIFFRACTIONr_angle_other_deg1.3371.5867748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5165448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.88219.202213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.99115540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1691547
X-RAY DIFFRACTIONr_chiral_restr0.0740.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024126
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02892
LS refinement shellResolution: 2.271→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 65 -
Rwork0.207 1488 -
all-1553 -
obs--96.82 %

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