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- PDB-3fwf: Ferric camphor bound cytochrome P450cam containing a Selenocystei... -

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Basic information

Entry
Database: PDB / ID: 3fwf
TitleFerric camphor bound cytochrome P450cam containing a Selenocysteine as the 5th heme ligand, monoclinic crystal form
ComponentsCamphor 5-monooxygenase
KeywordsOXIDOREDUCTASE / Selenocysteine / Hemoprotein / Cytochrome P450 / 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 / Resolution: 1.83 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 1.5Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_asym_id / _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_asym_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
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,98110
Polymers91,2882
Non-polymers1,6948
Water13,367742
1
A: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,4524
Polymers45,6441
Non-polymers8083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Camphor 5-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5306
Polymers45,6441
Non-polymers8865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.520, 61.930, 94.460
Angle α, β, γ (deg.)90.000, 90.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 45643.809 Da / Num. of mol.: 2 / 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CAM / CAMPHOR / Camphor


Mass: 152.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 742 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS A GLU -> GLN SEQUENCE CONFLICT AT RESIDUE 277 IN UNIPROT DATABASE.

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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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 24 % PEG 4000, 250 mM KCl, 50 mM TrisHCl, 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: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 26, 2008
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator, Dynamically bendable mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→45.64 Å / Num. all: 68937 / Num. obs: 68754 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.002 Å2 / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.83→1.93 Å / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 4 / Num. measured obs: 41864 / Num. unique obs: 10086 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCD detector softwaredata collection
XDSdata reduction
RefinementResolution: 1.83→45.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.16 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.881 / SU B: 2.566 / SU ML: 0.081 / SU R Cruickshank DPI: 0.136 / SU Rfree: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3318 4.8 %RANDOM
Rwork0.162 ---
all0.164 68753 --
obs0.164 65435 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.8 Å2 / Biso mean: 21.059 Å2 / Biso min: 4.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å2-0.11 Å2
2--0.24 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.83→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6402 0 112 742 7256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226778
X-RAY DIFFRACTIONr_angle_refined_deg1.5292.0129268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365829
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2123.994318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.787151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8651550
X-RAY DIFFRACTIONr_chiral_restr0.0990.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025276
X-RAY DIFFRACTIONr_nbd_refined0.2250.23583
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2646
X-RAY DIFFRACTIONr_metal_ion_refined0.1420.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.240
X-RAY DIFFRACTIONr_mcbond_it0.7741.54118
X-RAY DIFFRACTIONr_mcangle_it1.48826692
X-RAY DIFFRACTIONr_scbond_it2.52532678
X-RAY DIFFRACTIONr_scangle_it4.1334.52574
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 246 -
Rwork0.19 4827 -
all-5073 -
obs--100 %

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