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- PDB-3abb: Crystal structure of CYP105D6 -

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Basic information

Entry
Database: PDB / ID: 3abb
TitleCrystal structure of CYP105D6
ComponentsCytochrome P450 hydroxylase
KeywordsOXIDOREDUCTASE / P450 / heme / monooxygenase / macrolide / filipin / Iron / Metal-binding
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
PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 hydroxylase / Cytochrome P450
Similarity search - Component
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H.
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Regio- and stereospecificity of filipin hydroxylation sites revealed by crystal structures of cytochrome P450 105P1 and 105D6 from Streptomyces avermitilis
Authors: Xu, L.H. / Fushinobu, S. / Takamatsu, S. / Wakagi, T. / Ikeda, H. / Shoun, H.
#1: Journal: J.Bacteriol. / Year: 2009
Title: Crystal structures of cytochrome P450 105P1 from Streptomyces avermitilis: conformational flexibility and histidine ligation state
Authors: Xu, L.H. / Fushinobu, S. / Ikeda, H. / Wakagi, T. / Shoun, H.
History
DepositionDec 4, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: 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_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1932
Polymers44,5771
Non-polymers6161
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.533, 67.533, 182.089
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cytochrome P450 hydroxylase / CYP105D6


Mass: 44576.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: pteD, SAV412, SAV_412 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3)
References: UniProt: Q79ZT5, UniProt: Q93H80*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of ...References: UniProt: Q79ZT5, UniProt: Q93H80*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.69 Å3/Da / Density % sol: 54.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Sodium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 13, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 22279 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 32.8 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 25.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 4.1 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UED

1ued


Resolution: 2.3→33.77 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.924 / SU B: 11.023 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1133 5.1 %RANDOM
Rwork0.16023 ---
obs0.16325 21082 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.716 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.2557 Å
Refinement stepCycle: LAST / Resolution: 2.3→33.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 43 277 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0223073
X-RAY DIFFRACTIONr_angle_refined_deg2.0162.0144197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0175380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19423.404141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.24215476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5451526
X-RAY DIFFRACTIONr_chiral_restr0.1580.2462
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212386
X-RAY DIFFRACTIONr_mcbond_it1.0791.51908
X-RAY DIFFRACTIONr_mcangle_it1.97623069
X-RAY DIFFRACTIONr_scbond_it3.2631165
X-RAY DIFFRACTIONr_scangle_it5.014.51128
LS refinement shellResolution: 2.299→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 93 -
Rwork0.174 1503 -
obs--99.69 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.601-0.2148-0.35420.8481-0.03481.11520.10020.25150.2109-0.2183-0.0761-0.1579-0.0740.0861-0.0240.06030.02030.02860.05220.04730.0163-18.25436.65610.415
23.1866-0.71051.58981.0076-0.40240.79580.22930.4142-0.2627-0.1725-0.1411-0.03840.1620.1029-0.08810.09340.02530.00480.0695-0.03860.0313-19.26310.80221.858
31.0374-0.12960.33110.67760.07410.67810.06010.0754-0.0217-0.0483-0.07450.04190.0544-0.06840.01430.04550.00970.01940.054-0.00550.0305-16.85322.38222.264
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 92
2X-RAY DIFFRACTION2A93 - 192
3X-RAY DIFFRACTION3A193 - 408

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