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Basic information

Entry
Database: PDB / ID: 3w9c
TitleCrystal structure of the electron transfer complex of cytochrome p450cam with putidaredoxin
Components
  • Camphor 5-monooxygenase
  • Putidaredoxin
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / inter-protein electron transfer / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


P450-containing electron transport chain / camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / 2 iron, 2 sulfur cluster binding / electron transfer activity / iron ion binding / heme binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Cytochrome P450, B-class / Beta-grasp domain superfamily / Cytochrome p450 / Cytochrome P450 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. ...Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / Beta-grasp domain / 2Fe-2S iron-sulfur cluster binding domain / Cytochrome P450, B-class / Beta-grasp domain superfamily / Cytochrome p450 / Cytochrome P450 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Ubiquitin-like (UB roll) / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / PROTOPORPHYRIN IX CONTAINING FE / Camphor 5-monooxygenase / Putidaredoxin
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKikui, Y. / Hiruma, Y. / Hass, M.A. / Koteishi, H. / Ubbink, M. / Nojiri, M.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: The structure of the cytochrome p450cam-putidaredoxin complex determined by paramagnetic NMR spectroscopy and crystallography.
Authors: Hiruma, Y. / Hass, M.A. / Kikui, Y. / Liu, W.M. / Olmez, B. / Skinner, S.P. / Blok, A. / Kloosterman, A. / Koteishi, H. / Lohr, F. / Schwalbe, H. / Nojiri, M. / Ubbink, M.
History
DepositionApr 3, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_asym_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_seq_id / _struct_conn.ptnr1_label_asym_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
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Camphor 5-monooxygenase
B: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5359
Polymers58,2662
Non-polymers1,2697
Water63135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.717, 77.991, 60.016
Angle α, β, γ (deg.)90.00, 95.57, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 46664.973 Da / Num. of mol.: 1 / Mutation: K126C, R130C, C334A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Protein Putidaredoxin / PDX


Mass: 11601.094 Da / Num. of mol.: 1 / Mutation: C73S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00259

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Non-polymers , 5 types, 42 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.03 Å3/Da / Density % sol: 39.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES (PH7.5), 0.1M SODIUM CHLORIDE, 1.6M AMMONIUM SULFATE, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Feb 3, 2012
RadiationMonochromator: DOUBLE CRYSTAL SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→61.78 Å / Num. obs: 16251 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 19.4
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.6 / Rsym value: 0.44 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZWU, 1OQR

2zwu

1oqr


Resolution: 2.5→61.78 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.888 / SU B: 10.585 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25088 811 5 %RANDOM
Rwork0.18492 ---
all0.18829 16251 --
obs0.18829 15350 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å20 Å20.45 Å2
2---0.96 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→61.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 73 35 4078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224130
X-RAY DIFFRACTIONr_angle_refined_deg1.7532.0035627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8665504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.61424.167192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.07515673
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4151530
X-RAY DIFFRACTIONr_chiral_restr0.1140.2614
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213173
X-RAY DIFFRACTIONr_mcbond_it0.771.52536
X-RAY DIFFRACTIONr_mcangle_it1.50624110
X-RAY DIFFRACTIONr_scbond_it2.34431594
X-RAY DIFFRACTIONr_scangle_it3.8394.51515
LS refinement shellResolution: 2.501→2.566 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 57 -
Rwork0.213 1109 -
obs-1109 98.23 %

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