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- PDB-1mpw: Molecular Recognition in (+)-a-Pinene Oxidation by Cytochrome P450cam -

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Basic information

Entry
Database: PDB / ID: 1mpw
TitleMolecular Recognition in (+)-a-Pinene Oxidation by Cytochrome P450cam
ComponentsCYTOCHROME P450CAM
KeywordsOXIDOREDUCTASE / P450cam / (+)-Pinene
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
PROTOPORPHYRIN IX CONTAINING FE / : / (+)-alpha-Pinene / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsBell, S.G. / Chen, X. / Sowden, R.J. / Xu, F. / Willams, J.N. / Wong, L.-L. / Rao, Z.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Molecular recognition in (+)-alpha-pinene oxidation by cytochrome P450cam
Authors: Bell, S.G. / Chen, X. / Sowden, R.J. / Xu, F. / Williams, J.N. / Wong, L.-L. / Rao, Z.
History
DepositionSep 13, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 31, 2014Group: Non-polymer description
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME P450CAM
B: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7718
Polymers93,1882
Non-polymers1,5846
Water1,928107
1
A: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3864
Polymers46,5941
Non-polymers7923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME P450CAM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3864
Polymers46,5941
Non-polymers7923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.903, 62.517, 95.698
Angle α, β, γ (deg.)90.00, 90.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CYTOCHROME P450CAM / Camphor 5-monooxygenase


Mass: 46593.879 Da / Num. of mol.: 2 / Mutation: F87W/Y96F/V247L/C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Cell line (production host): JM109 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-TMH / (+)-alpha-Pinene / (+)-3,6,6-TRIMETHYLBICYCLO[3.1.1]HEPT-2-ENE


Mass: 136.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: PEG8000, sodium acetate, sodium cacodylate, pH 6.5, EVAPORATION, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMcacodylate1droppH6.5
2200 mM1dropKCl
38 mg/mlprotein1drop
430 %PEG80001reservoir
5100 mMcacodylate1reservoirpH6.5
6200 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 14, 2002
RadiationMonochromator: Osmic Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.34→41.28 Å / Num. all: 32999 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 19.4 Å2 / Limit h max: 28 / Limit h min: -28 / Limit k max: 26 / Limit k min: -28 / Limit l max: 40 / Limit l min: 0 / Observed criterion F max: 242279.83 / Observed criterion F min: 0.55
Reflection shellResolution: 2.33→2.41 Å / % possible all: 95.8
Reflection
*PLUS
Num. obs: 33002 / % possible obs: 97.1 % / Num. measured all: 300428 / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
% possible obs: 84.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→41.28 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3187 10 %random
Rwork0.204 ---
all-33719 --
obs-31917 94.7 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 22.1476 Å2 / ksol: 0.335132 e/Å3
Displacement parametersBiso max: 51.65 Å2 / Biso mean: 21.32 Å2 / Biso min: 2.49 Å2
Baniso -1Baniso -2Baniso -3
1-3.86 Å20 Å21.85 Å2
2---3.68 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.23 Å
Luzzati d res high-2.34
Refinement stepCycle: LAST / Resolution: 2.34→41.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 108 107 6635
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_torsion_deg22.4
X-RAY DIFFRACTIONx_torsion_impr_deg1.48
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.34-2.440.2453418.20.24633220.0134174366387.8
2.44-2.570.2263728.90.22834760.0124192384891.8
2.57-2.730.2364039.60.23934770.0124183388092.8
2.73-2.950.2314009.50.2335960.0124224399694.6
2.95-3.240.2294069.70.22636000.0114191400695.6
3.24-3.710.2194159.80.21437060.0114219412197.7
3.71-4.670.171424100.16837360.0084227416098.4
4.67-41.280.1624269.80.16838170.0084340424397.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4hem.paramhem.top
X-RAY DIFFRACTION5pp.parampp.top
Refinement
*PLUS
% reflection Rfree: 8 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS

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