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- PDB-4wq0: Crystal structure of cytochrome P450 CYP107W1 from Streptomyces a... -

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Basic information

Entry
Database: PDB / ID: 4wq0
TitleCrystal structure of cytochrome P450 CYP107W1 from Streptomyces avermitilis in complex with Oligomycin A
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE/ANTIBIOTIC / P450 / CYP / CYP107W1 / Streptomyces avermitilis / oligomycin / OXIDOREDUCTASE-ANTIBIOTIC complex
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 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Oligomycin A / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
Model detailsBiosynthesis of Oligomycin A
AuthorsKang, L.W. / Kim, D.H. / Pham, T.V. / Han, S.H.
CitationJournal: To Be Published
Title: Crystal structure of cytochrome P450 CYP107W1 from Streptomyces avermitilis in complex with Oligomycin A
Authors: Kang, L.W. / Kim, D.H. / Pham, T.V. / Han, S.H. / Kim, J.H. / Lim, Y.R. / Park, H.G. / Cha, G.S. / Yun, C.H. / Chun, Y.J.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7223
Polymers43,3151
Non-polymers1,4082
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.812, 127.812, 76.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-602-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Cytochrome P450 / CYP107W1


Mass: 43314.551 Da / Num. of mol.: 1 / Fragment: UNP residues 8-404
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Gene: olmB / Plasmid: pET 28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q93HJ0
#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-EFO / Oligomycin A / (1R,4E,5'S,6S,6'S,7R,8S,10R,11R,12S,14R,15S,16R,18E,20E,22R,25S,27R,28S,29R)-22-ethyl-7,11,14,15-tetrahydroxy-6'-[(2R)-2-hydroxypropyl]-5',6,8,10,12,14,16,28,29-nonamethyl-3',4',5',6'-tetrahydro-3H,9H,13H-spiro[2,26-dioxabicyclo[23.3.1]nonacosa-4,18,20-triene-27,2'-pyran]-3,9,13-trione


Mass: 791.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H74O11 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: Isopropanol, Ammonium citrate, citric acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 20, 2013 / Details: mirror
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19627 / % possible obs: 99.6 % / Redundancy: 8.8 % / Net I/σ(I): 26.2

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0049refinement
SCALEPACKdata reduction
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.7→40.42 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.907 / SU B: 19.374 / SU ML: 0.352 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2885 891 5.2 %RANDOM
Rwork0.2154 16238 --
obs0.2191 16238 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.89 Å2 / Biso mean: 79.432 Å2 / Biso min: 47.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20 Å2
2---0.05 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 2.7→40.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 99 15 3157
Biso mean--90.47 61.5 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193206
X-RAY DIFFRACTIONr_bond_other_d0.0010.023158
X-RAY DIFFRACTIONr_angle_refined_deg1.9152.0264388
X-RAY DIFFRACTIONr_angle_other_deg0.87737272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2595396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.55724.186129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.10115530
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4731525
X-RAY DIFFRACTIONr_chiral_restr0.0840.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213547
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02651
X-RAY DIFFRACTIONr_mcbond_it4.6097.6791587
X-RAY DIFFRACTIONr_mcbond_other4.6067.6781586
X-RAY DIFFRACTIONr_mcangle_it7.211.5131982
LS refinement shellResolution: 2.703→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 61 -
Rwork0.406 1061 -
all-1122 -
obs--85.98 %

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