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- PDB-3wec: Structure of P450 RauA (CYP1050A1) complexed with a biosynthetic ... -

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Basic information

Entry
Database: PDB / ID: 3wec
TitleStructure of P450 RauA (CYP1050A1) complexed with a biosynthetic intermediate of aurachin RE
ComponentsCytochrome P450
KeywordsOXIDOREDUCTASE / P450 fold / monooxygenase (hydroxylase) / heme / Cytosolic enzyme
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 / Cytochrome P450 superfamily / Cytochrome P450 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-AUI / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450
Similarity search - Component
Biological speciesRhodococcus erythropolis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsYasutake, Y. / Kitagawa, W. / Tamura, T.
CitationJournal: Febs Lett. / Year: 2014
Title: Structure of the quinoline N-hydroxylating cytochrome P450 RauA, an essential enzyme that confers antibiotic activity on aurachin alkaloids
Authors: Yasutake, Y. / Kitagawa, W. / Hata, M. / Nishioka, T. / Ozaki, T. / Nishiyama, M. / Kuzuyama, T. / Tamura, T.
History
DepositionJul 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,9123
Polymers45,9161
Non-polymers9962
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.460, 100.040, 52.290
Angle α, β, γ (deg.)90.00, 108.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cytochrome P450


Mass: 45916.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis (bacteria) / Strain: JCM 6824 / Gene: rauA / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S6BVH1
#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-AUI / 3-[(2E,6E,9R)-9-hydroxy-3,7,11-trimethyldodeca-2,6,10-trien-1-yl]-2-methylquinolin-4(1H)-one / Dehydroxy-aurachin RE


Mass: 379.535 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H33NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.24 Å3/Da / Density % sol: 45.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES buffer pH 6.5, 12% PEG20000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 20745 / Num. obs: 20745 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 11.4
Reflection shellResolution: 2.19→2.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3 / Num. unique all: 3016 / % possible all: 99.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: P450 BioI fragment (PDB code, 3ejd)

3ejd


Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.97 / SU ML: 0.208 / Cross valid method: THROUGHOUT / ESU R: 0.326 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26318 1065 5.1 %RANDOM
Rwork0.21378 ---
obs0.21638 19658 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.752 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å20 Å2-4 Å2
2---1.1 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3073 0 71 54 3198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193220
X-RAY DIFFRACTIONr_angle_refined_deg2.391.9924389
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4325402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34323.077143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.87315507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6881530
X-RAY DIFFRACTIONr_chiral_restr0.1240.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212487
LS refinement shellResolution: 2.19→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 68 -
Rwork0.262 1402 -
obs--98.59 %
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)
16.15140.82334.12535.52090.40374.918-0.38710.52321.0002-0.3455-0.0540.5604-1.153-0.02650.44110.59850.0638-0.0130.39930.22110.3523-1.863213.74145.514
27.7172-1.5859-5.54011.74461.11194.11940.2002-0.60560.59990.2764-0.1004-0.3056-0.36220.4102-0.09980.7124-0.0521-0.30880.1992-0.09920.85834.324815.517425.1095
35.96110.95732.59083.65841.12833.68770.6054-0.512-0.60470.1548-0.20570.01630.5368-0.0584-0.39960.1488-0.0481-0.00870.15270.03060.15732.7802-6.104725.9496
45.50831.0271.96872.61510.00534.05320.1470.81520.0807-0.5849-0.11170.4297-0.11330.3032-0.03530.23890.0903-0.04090.2542-0.02440.1352-0.3096-1.63169.1468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 64
2X-RAY DIFFRACTION2A65 - 107
3X-RAY DIFFRACTION3A108 - 284
4X-RAY DIFFRACTION4A285 - 411

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