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- PDB-1p2y: CRYSTAL STRUCTURE OF CYTOCHROME P450CAM IN COMPLEX WITH (S)-(-)-N... -

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Basic information

Entry
Database: PDB / ID: 1p2y
TitleCRYSTAL STRUCTURE OF CYTOCHROME P450CAM IN COMPLEX WITH (S)-(-)-NICOTINE
ComponentsCytochrome P450-cam
KeywordsOXIDOREDUCTASE / MONOOXYGENASE / HEME / NICOTINE
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
PROTOPORPHYRIN IX CONTAINING FE / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsStrickler, M. / Goldstein, B.M. / Maxfield, K. / Shireman, L. / Kim, G. / Matteson, D. / Jones, J.P.
CitationJournal: Biochemistry / Year: 2003
Title: Crystallographic Studies on the Complex Behavior of Nicotine Binding to P450cam (CYP101)(dagger).
Authors: Strickler, M. / Goldstein, B.M. / Maxfield, K. / Shireman, L. / Kim, G. / Matteson, D. / Jones, J.P.
History
DepositionApr 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450-cam
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1963
Polymers47,4181
Non-polymers7792
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.050, 64.050, 251.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 47417.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: CAMC OR CYP101 / Plasmid: pBLUESCRIPT / Production host: Escherichia coli (E. coli) / Strain (production host): DH5ALPHA / References: UniProt: P00183, camphor 5-monooxygenase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NCT / (S)-3-(1-METHYLPYRROLIDIN-2-YL)PYRIDINE / (S)-(-)-NICOTINE / 3-[(2S)-1-METHYL-2-PYRROLIDINYL] PYRIDINE / Nicotine


Mass: 162.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2 / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.7 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 8000, potassium phosphate, potassium chloride, dithiothreitol, nicotine, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116-24 %(w/v)PEG80001reservoir
220-30 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 7, 1996
RadiationMonochromator: Si (III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→39.52 Å / Num. all: 25149 / Num. obs: 21616 / % possible obs: 86 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 13 Å2 / Rsym value: 0.066 / Net I/σ(I): 12.4
Reflection shellResolution: 2.3→2.32 Å / Mean I/σ(I) obs: 4 / Num. unique all: 334 / Rsym value: 0.242 / % possible all: 56.4
Reflection
*PLUS
Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 56.4 % / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→39.52 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 441226.16 / Data cutoff high rms absF: 441226.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2056 9.8 %RANDOM
Rwork0.223 ---
all0.25 21287 --
obs0.223 20892 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.9252 Å2 / ksol: 0.321998 e/Å3
Displacement parametersBiso mean: 23.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2--1.11 Å20 Å2
3----2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 55 122 3404
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.43
X-RAY DIFFRACTIONc_mcbond_it2.761.5
X-RAY DIFFRACTIONc_mcangle_it4.282
X-RAY DIFFRACTIONc_scbond_it5.632
X-RAY DIFFRACTIONc_scangle_it8.082.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.28 241 9.4 %
Rwork0.245 2310 -
obs-2551 64.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_S_NOVDW.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HEME19X_NOVDW_FEBONDS.PARAMHEMEIII_FEBONDS.TOP
X-RAY DIFFRACTION3NICOTINE_NOVDW.PARAMNICOTINE.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Rfactor Rfree: 0.264
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.439
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.066
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.428

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