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Basic information

Entry
Database: PDB / ID: 5gxg
TitleHigh-resolution crystal 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / 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: 1.7 Å
AuthorsKikui, Y. / Hiruma, Y. / Ubbink, M. / Nojiri, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Identification of productive and futile encounters in an electron transfer protein complex
Authors: Andraojc, W. / Hiruma, Y. / Liu, W.M. / Ravera, E. / Nojiri, M. / Parigi, G. / Luchinat, C. / Ubbink, M.
History
DepositionSep 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)59,70910
Polymers58,2822
Non-polymers1,4278
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-112 kcal/mol
Surface area21000 Å2
2
A: Camphor 5-monooxygenase
B: Putidaredoxin
hetero molecules

A: Camphor 5-monooxygenase
B: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,41820
Polymers116,5644
Non-polymers2,85416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7270 Å2
ΔGint-132 kcal/mol
Surface area40060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.490, 77.956, 59.968
Angle α, β, γ (deg.)90.00, 95.51, 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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Protein Putidaredoxin / PDX


Mass: 11617.159 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camB / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00259

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Non-polymers , 5 types, 302 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.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#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.: 294 / 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: 39.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES, 0.1M Sodium Chloride, 1.6M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→61.66 Å / Num. obs: 51169 / % possible obs: 99.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 39.2
Reflection shellResolution: 1.7→1.73 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3w9c

3w9c


Resolution: 1.7→59.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.024 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19158 2579 5.1 %RANDOM
Rwork0.15603 ---
obs0.15788 48328 99.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.446 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å2-0.01 Å2
2---0.1 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.7→59.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3970 0 80 294 4344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194165
X-RAY DIFFRACTIONr_bond_other_d0.0010.023905
X-RAY DIFFRACTIONr_angle_refined_deg2.1371.9865678
X-RAY DIFFRACTIONr_angle_other_deg0.99638996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2375512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19624.093193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78215682
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2481531
X-RAY DIFFRACTIONr_chiral_restr0.1360.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214706
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02939
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4032.4632033
X-RAY DIFFRACTIONr_mcbond_other2.4022.4632032
X-RAY DIFFRACTIONr_mcangle_it3.223.6832538
X-RAY DIFFRACTIONr_mcangle_other3.223.6832539
X-RAY DIFFRACTIONr_scbond_it3.9552.8942132
X-RAY DIFFRACTIONr_scbond_other3.9492.8942132
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7244.1773135
X-RAY DIFFRACTIONr_long_range_B_refined6.81720.7154897
X-RAY DIFFRACTIONr_long_range_B_other6.75620.4384792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.699→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 189 -
Rwork0.214 3469 -
obs--97.24 %

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