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- PDB-3wrk: Crystal structure of P450cam -

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Basic information

Entry
Database: PDB / ID: 3wrk
TitleCrystal structure of P450cam
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / Metal-binding
Function / homology
Function and homology information


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / iron ion binding / heme binding / cytoplasm
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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.609 Å
AuthorsKishimoto, A. / Takagi, K. / Amano, A. / Sakurai, K. / Mizushima, T. / Shimada, H.
CitationJournal: To be Published
Title: Structure of P450cam intermedite
Authors: Kishimoto, A. / Takagi, K. / Amano, A. / Sakurai, K. / Katayama, Y. / Aminaka, R. / Ito, M. / Mizushima, T. / Shimada, H.
History
DepositionFeb 25, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 18, 2015Provider: 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: Camphor 5-monooxygenase
D: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6356
Polymers95,0982
Non-polymers1,5374
Water3,063170
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3183
Polymers47,5491
Non-polymers7692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
D: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3183
Polymers47,5491
Non-polymers7692
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.339, 93.188, 73.828
Angle α, β, γ (deg.)90.00, 89.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Camphor 5-monooxygenase / Cytochrome P450-cam / Cytochrome P450cam


Mass: 47548.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: PUC18 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.65 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM Tris-HCl, 200mM KCl, 20-30% PEG 4000, 0.00025mM Camphor, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jan 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 24893 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 14.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L62

3l62


Resolution: 2.609→39.403 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.875 / SU ML: 0.33 / σ(F): 1.37 / Phase error: 24.69 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2353 1260 5.07 %
Rwork0.1737 --
obs0.1769 24841 99.49 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.485 Å2 / ksol: 0.316 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.7022 Å20 Å2-0.0678 Å2
2---0.1264 Å2-0 Å2
3----0.5758 Å2
Refinement stepCycle: LAST / Resolution: 2.609→39.403 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6217 0 108 170 6495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156520
X-RAY DIFFRACTIONf_angle_d1.7658897
X-RAY DIFFRACTIONf_dihedral_angle_d16.9232428
X-RAY DIFFRACTIONf_chiral_restr0.11955
X-RAY DIFFRACTIONf_plane_restr0.0111167
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6094-2.71390.26081470.1982523X-RAY DIFFRACTION96
2.7139-2.83740.29231380.20832616X-RAY DIFFRACTION100
2.8374-2.98690.33331330.20262615X-RAY DIFFRACTION100
2.9869-3.1740.23841420.18232632X-RAY DIFFRACTION100
3.174-3.41890.23361160.18022618X-RAY DIFFRACTION100
3.4189-3.76270.21561510.15372623X-RAY DIFFRACTION100
3.7627-4.30660.23081370.152638X-RAY DIFFRACTION100
4.3066-5.42360.20061600.15532624X-RAY DIFFRACTION100
5.4236-39.40740.21731360.18462692X-RAY DIFFRACTION100

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