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- PDB-3p6r: Crystal Structure of Cytochrome P450cam crystallized in the prese... -

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Basic information

Entry
Database: PDB / ID: 3p6r
TitleCrystal Structure of Cytochrome P450cam crystallized in the presence of a tethered substrate analog 3OH-AdaC1-Etg-Boc
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
PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 3OH-AdaC1-Etg-Boc
Authors: Lee, Y.-T. / Glazer, E.C. / Wilson, R.F. / Goodin, D.B.
History
DepositionOct 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2093
Polymers46,5571
Non-polymers6522
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.809, 75.008, 91.781
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 / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
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: BL7-1 / Wavelength: 0.97839 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 6, 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: 0.97839 Å / Relative weight: 1
ReflectionResolution: 2.1→91.781 Å / Num. all: 27625 / Num. obs: 27551 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.111 / Rsym value: 0.111 / Net I/σ(I): 13.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.215.70.830.92233639420.8399.9
2.21-2.355.60.5841.32122437700.58499.9
2.35-2.515.60.4181.81977835300.418100
2.51-2.715.60.2792.71835432990.27999.9
2.71-2.975.60.1913.91698830420.19199.9
2.97-3.325.60.1146.41557327870.11499.9
3.32-3.835.50.06310.91356224620.063100
3.83-4.75.40.05111.21134821140.05199.9
4.7-6.645.10.0658.8835016490.06599.3
6.64-29.0375.30.03416.550859560.03498.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.31 Å28.96 Å
Translation2.31 Å28.96 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 / Resolution: 2.1→10 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.2026 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8378 / SU B: 5.024 / SU ML: 0.134 / SU R Cruickshank DPI: 0.2347 / SU Rfree: 0.1868 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1374 5 %RANDOM
Rwork0.2167 ---
obs0.2182 27265 99.84 %-
all-27625 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.7 Å2 / Biso mean: 37.0613 Å2 / Biso min: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å2-0 Å2-0 Å2
2---0.49 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 44 81 3276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223282
X-RAY DIFFRACTIONr_angle_refined_deg1.2992.0074475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.575398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.87923.935155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34115541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4071525
X-RAY DIFFRACTIONr_chiral_restr0.0880.2483
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212539
X-RAY DIFFRACTIONr_mcbond_it0.5831.51997
X-RAY DIFFRACTIONr_mcangle_it1.13623239
X-RAY DIFFRACTIONr_scbond_it1.83931285
X-RAY DIFFRACTIONr_scangle_it3.0234.51235
LS refinement shellResolution: 2.1→2.152 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 86 -
Rwork0.266 1824 -
all-1910 -
obs-1824 99.79 %

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