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- PDB-3fwi: Ferric camphor bound Cytochrome P450cam containing a selenocystei... -

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Basic information

Entry
Database: PDB / ID: 3fwi
TitleFerric camphor bound Cytochrome P450cam containing a selenocysteine as the 5th heme ligand, tetragonal crystal form
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / Hemoprotein / cytochrome P450 / selenocysteine / Cytochrome / Heme / Iron / Metal-binding / Monooxygenase
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 / Rigid Body in Refmac starting from pdb entry 1yrc / Resolution: 2.4 Å
AuthorsSchlichting, I. / von Koenig, K. / Aldag, C. / Hilvert, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Probing the role of the proximal heme ligand in cytochrome P450cam by recombinant incorporation of selenocysteine.
Authors: Aldag, C. / Gromov, I.A. / Garcia-Rubio, I. / von Koenig, K. / Schlichting, I. / Jaun, B. / Hilvert, D.
History
DepositionJan 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Other
Revision 1.3Aug 6, 2014Group: Other
Revision 1.4Nov 1, 2017Group: Refinement description / Category: software
Revision 1.5Sep 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 / 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 / _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: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4534
Polymers45,6451
Non-polymers8083
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.580, 63.580, 243.140
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 Camphor 5-monooxygenase / Cytochrome P450-cam / Cytochrome P450cam


Mass: 45644.793 Da / Num. of mol.: 1 / Mutation: C357U, R365L, E366Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Production host: Escherichia coli (E. coli) / 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-CAM / CAMPHOR


Mass: 152.233 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 290 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 24 % PEG 4000, 250 mM KCl, 50 mM Tris HCl, cryoprotection by addition of 20 % glycerol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98158 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 21, 2006
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98158 Å / Relative weight: 1
ReflectionResolution: 2.4→44.95 Å / Num. obs: 19089 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.106
Reflection shellResolution: 2.4→2.5 Å / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4.07 / Num. unique all: 2294 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MAR345CCD detector softwaredata collection
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: Rigid Body in Refmac starting from pdb entry 1yrc
Starting model: pdb entry 1yrc

1yrc


Resolution: 2.4→44.95 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.899 / SU B: 7.372 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23817 1001 5 %RANDOM
Rwork0.17601 ---
all0.179 19089 --
obs0.179 19089 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.957 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2---0.81 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→44.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3205 0 55 290 3550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223347
X-RAY DIFFRACTIONr_angle_refined_deg1.8552.0124567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6995404
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38123.987158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.34415547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7181525
X-RAY DIFFRACTIONr_chiral_restr0.1210.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022591
X-RAY DIFFRACTIONr_nbd_refined0.2290.21702
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22239
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2261
X-RAY DIFFRACTIONr_metal_ion_refined0.1180.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.215
X-RAY DIFFRACTIONr_mcbond_it0.7791.52031
X-RAY DIFFRACTIONr_mcangle_it1.48323292
X-RAY DIFFRACTIONr_scbond_it2.65831325
X-RAY DIFFRACTIONr_scangle_it4.0934.51275
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 72 -
Rwork0.179 1394 -
obs--100 %

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