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- PDB-2zwu: Crystal Structure of Camphor Soaked Ferric Cytochrome P450cam -

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Basic information

Entry
Database: PDB / ID: 2zwu
TitleCrystal Structure of Camphor Soaked Ferric Cytochrome P450cam
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / P450CAM / MONOOXYGENASE / CAMPHOR-HYDROXYLASE / HEME / IRON / METAL-BINDING / SUBSTRATE-SOAKING / Cytoplasm
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
CAMPHOR / PROTOPORPHYRIN IX CONTAINING FE / : / Camphor 5-monooxygenase
Similarity search - Component
Biological speciesPseudomonas Putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSakurai, K. / Shimada, H. / Hayashi, T. / Tsukihara, T.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Substrate binding induces structural changes in cytochrome P450cam
Authors: Sakurai, K. / Shimada, H. / Hayashi, T. / Tsukihara, T.
History
DepositionDec 18, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)47,6505
Polymers46,7201
Non-polymers9304
Water14,340796
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.608, 63.608, 250.389
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 46720.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas Putida (bacteria) / Strain: cyp101 / Gene: camc / Plasmid: M13tv19 / Production host: Escherichia coli (E. coli) / Strain (production host): Jm109 / References: UniProt: P00183, camphor 5-monooxygenase

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Non-polymers , 5 types, 800 molecules

#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-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 796 / 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: 2.71 Å3/Da / Density % sol: 54.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 11-14% PEG 4000, 50mM Tris-HCl, 250mM KCl, 1mM d-camphor, 10mM dithioerythritol(DTE); After crystallization, soaked camphor saturated buffer for 2 days, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.7 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Apr 22, 2008 / Details: Si
RadiationMonochromator: Silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.3→34.9 Å / Num. obs: 125182 / % possible obs: 98.6 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.597 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 34.4
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 5 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 4.9 / Num. unique all: 12324 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREP9.4.09phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CPP

2cpp


Resolution: 1.3→34.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.676 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18386 6277 5 %RANDOM
Rwork0.16552 ---
obs0.16644 118839 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.699 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4715 0 66 806 5587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223966
X-RAY DIFFRACTIONr_bond_other_d0.0020.02963
X-RAY DIFFRACTIONr_angle_refined_deg1.52.0115498
X-RAY DIFFRACTIONr_angle_other_deg1.35432507
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5855536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.31924.271192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.51115696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2111531
X-RAY DIFFRACTIONr_chiral_restr0.0840.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024597
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02465
X-RAY DIFFRACTIONr_nbd_refined0.2140.21906
X-RAY DIFFRACTIONr_nbd_other0.220.21639
X-RAY DIFFRACTIONr_nbtor_refined0.240.22537
X-RAY DIFFRACTIONr_nbtor_other0.1750.21668
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2648
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.265
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.256
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5751.52394
X-RAY DIFFRACTIONr_mcbond_other0.1551.5856
X-RAY DIFFRACTIONr_mcangle_it1.03923973
X-RAY DIFFRACTIONr_scbond_it1.56631582
X-RAY DIFFRACTIONr_scangle_it2.344.51495
X-RAY DIFFRACTIONr_rigid_bond_restr0.60731
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded5.878326
LS refinement shellResolution: 1.302→1.336 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 454 -
Rwork0.229 8496 -
obs--98.05 %

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