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- PDB-3wri: Crystal structure of P450cam -

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Basic information

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


camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol 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: 2.9 Å
AuthorsKishimoto, A. / Takagi, K. / Amano, A. / Sakurai, K. / Mizushima, T. / Shimada, H.
CitationJournal: To be Published
Title: Structure of P450cam intermediate
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

Downloads & links

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Assembly

Deposited unit
A: Camphor 5-monooxygenase
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6356
Polymers95,0982
Non-polymers1,5374
Water1629
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
B: 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)61.440, 74.227, 92.636
Angle α, β, γ (deg.)90.00, 89.98, 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.: 9 / 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: 2.22 Å3/Da / Density % sol: 44.62 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 50mM Tris-HCl, 200mM KCl,20-30% PEG 4000, 0.001mM 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: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 18663 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.8
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 5.8 / % 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: 2.9→46.318 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.819 / SU ML: 0.4 / σ(F): 1.35 / Phase error: 27.35 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2675 953 5.11 %
Rwork0.1896 --
obs0.1935 18640 99.82 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 11.727 Å2 / ksol: 0.278 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5718 Å20 Å20.0104 Å2
2--0.5084 Å2-0 Å2
3---0.0634 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6395 0 108 9 6512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156758
X-RAY DIFFRACTIONf_angle_d1.8389236
X-RAY DIFFRACTIONf_dihedral_angle_d18.3582542
X-RAY DIFFRACTIONf_chiral_restr0.116992
X-RAY DIFFRACTIONf_plane_restr0.0121211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8998-3.05270.38761430.28292486X-RAY DIFFRACTION99
3.0527-3.24390.33361200.25082513X-RAY DIFFRACTION100
3.2439-3.49430.32141440.21652530X-RAY DIFFRACTION100
3.4943-3.84580.2571540.17692507X-RAY DIFFRACTION100
3.8458-4.40190.22661410.15262515X-RAY DIFFRACTION100
4.4019-5.54450.23811220.16132545X-RAY DIFFRACTION100
5.5445-46.32390.22491290.17832591X-RAY DIFFRACTION100

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