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- PDB-3oia: Crystal Structure of Cytochrome P450cam crystallized in the prese... -

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Basic information

Entry
Database: PDB / ID: 3oia
TitleCrystal Structure of Cytochrome P450cam crystallized in the presence of a tethered substrate analog AdaC1-C8GluEtg-Bio
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / Cytochrome P450 / P450cam / camphor / tethered substrate analog / open conformation
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
Chem-A31 / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLee, Y.-T. / Wilson, R.F. / Glazer, E.C. / Goodin, D.B.
CitationJournal: To be Published
Title: Crystal Structure of Cytochrome P450cam crystallized in the presence of a tethered substrate analog AdaC1-C8GluEtg-Bio
Authors: Lee, Y.-T. / Glazer, E.C. / Wilson, R.F. / Goodin, D.B.
History
DepositionAug 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / 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_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_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_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_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_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0624
Polymers46,5571
Non-polymers1,5053
Water8,683482
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.258, 75.089, 93.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46556.816 Da / Num. of mol.: 1 / Fragment: Full length / Mutation: C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase
#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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-A31 / N-{15-oxo-19-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]-4,7,10-trioxa-14-azanonadec-1-yl}-N'-(8-{[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbonyl]amino}octyl)pentanediamide


Mass: 849.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H76N6O8S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 279 K / Method: sitting-drop vapor diffusion / pH: 6.5
Details: 12-22% PEG 8000, 0.1M Sodium cacodylate, pH 6.5, 0.1-0.2M KCl, sitting-drop vapor diffusion, temperature 279K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 16, 2007 / Details: RH COATED FLAT MIRROR
RadiationMonochromator: SIDE SCATTERING I-BEAM BENT SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.6→93.25 Å / Num. all: 61156 / Num. obs: 52340 / % possible obs: 86.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.70.4521.42661271450.45281.9
1.69-1.793.80.2932.52567667740.29381.9
1.79-1.913.80.1823.72422663810.18281.9
1.91-2.073.80.1186.12252259920.11882.4
2.07-2.263.70.07792047955740.07783.3
2.26-2.533.60.0659.81885052950.06587
2.53-2.923.50.04414.81769450800.04493.8
2.92-3.583.50.03815.81608545320.03897.9
3.58-5.063.50.0319.91242735210.0397.3
5.06-39.593.70.03118.9748420460.03197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2 Å39.59 Å
Translation2 Å39.59 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RE9

1re9


Resolution: 1.65→10 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2221 / WRfactor Rwork: 0.1796 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8616 / SU B: 1.885 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1176 / SU Rfree: 0.12 / Cross valid method: THROUGHOUT / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 2441 5.1 %RANDOM
Rwork0.1871 ---
obs0.1894 47773 86.02 %-
all-55849 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 50.81 Å2 / Biso mean: 20.6765 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å2-0 Å20 Å2
2--0.38 Å2-0 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 74 482 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223422
X-RAY DIFFRACTIONr_angle_refined_deg1.3672.0154672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6735419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.29523.889162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26315566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2361527
X-RAY DIFFRACTIONr_chiral_restr0.0990.2501
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212649
X-RAY DIFFRACTIONr_mcbond_it0.6911.52058
X-RAY DIFFRACTIONr_mcangle_it1.25123343
X-RAY DIFFRACTIONr_scbond_it1.98631364
X-RAY DIFFRACTIONr_scangle_it3.2644.51323
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 174 -
Rwork0.224 3037 -
all-3211 -
obs-3962 81.04 %

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