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- PDB-4jws: Crystal structure of Cytochrome P450cam-putidaredoxin complex -

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Basic information

Entry
Database: PDB / ID: 4jws
TitleCrystal structure of Cytochrome P450cam-putidaredoxin complex
Components
  • Camphor 5-monooxygenase
  • Putidaredoxin
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / P450cam-Pdx complex / redox partners / 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 / iron ion binding / heme binding / metal ion binding / cytosol / cytoplasm
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 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily ...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 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Cytochrome p450 / Cytochrome P450 / 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
1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione / 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: 2.15 Å
AuthorsTripathi, S.M. / Li, H. / Poulos, T.L.
CitationJournal: Science / Year: 2013
Title: Structural basis for effector control and redox partner recognition in cytochrome P450.
Authors: Tripathi, S. / Li, H. / Poulos, T.L.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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_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.pdbx_leaving_atom_flag / _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_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)119,93612
Polymers117,7114
Non-polymers2,2258
Water4,161231
1
A: Camphor 5-monooxygenase
C: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9686
Polymers58,8562
Non-polymers1,1134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Camphor 5-monooxygenase
D: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9686
Polymers58,8562
Non-polymers1,1134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.590, 106.720, 88.700
Angle α, β, γ (deg.)90.00, 107.91, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 46597.715 Da / Num. of mol.: 2 / Mutation: K344C, C334A, C59S, C86S, C137S, C286S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: camC, cyp101 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00183, camphor 5-monooxygenase
#2: Protein Putidaredoxin / PDX


Mass: 12257.790 Da / Num. of mol.: 2
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, 239 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-1N0 / 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione / bis(maleimido)hexane, bound form


Mass: 280.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N2O4
#6: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2S2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.2 Å3/Da / Density % sol: 44.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2 M calcium acetate hydrate, 14-22% PEG3350, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.02 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.15→54.8 Å / Num. obs: 55488 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.103 / Rsym value: 0.103 / Net I/σ(I): 7.1
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 2 / Rsym value: 0.792 / % possible all: 100

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2CPP AND 1XLO

2cpp

1xlo


Resolution: 2.15→54.799 Å / SU ML: 0.25 / σ(F): 1.33 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.225 2775 5.01 %
Rwork0.1751 --
obs0.1776 55382 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→54.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7787 0 136 231 8154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098121
X-RAY DIFFRACTIONf_angle_d1.25611063
X-RAY DIFFRACTIONf_dihedral_angle_d13.9652999
X-RAY DIFFRACTIONf_chiral_restr0.0491209
X-RAY DIFFRACTIONf_plane_restr0.0061449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.18710.28251310.23122640X-RAY DIFFRACTION100
2.1871-2.22680.30661240.24192651X-RAY DIFFRACTION100
2.2268-2.26970.36971540.28792542X-RAY DIFFRACTION98
2.2697-2.3160.26861200.23942640X-RAY DIFFRACTION99
2.316-2.36640.23491560.20662581X-RAY DIFFRACTION100
2.3664-2.42140.26441430.19732639X-RAY DIFFRACTION100
2.4214-2.4820.27391260.19772640X-RAY DIFFRACTION100
2.482-2.54910.28881230.20372620X-RAY DIFFRACTION100
2.5491-2.62410.22471590.19392637X-RAY DIFFRACTION100
2.6241-2.70880.29321330.20152607X-RAY DIFFRACTION100
2.7088-2.80560.28661390.20142626X-RAY DIFFRACTION100
2.8056-2.91790.27271300.20292638X-RAY DIFFRACTION100
2.9179-3.05070.27021630.20152614X-RAY DIFFRACTION100
3.0507-3.21150.23961240.18682647X-RAY DIFFRACTION100
3.2115-3.41270.2421550.18282617X-RAY DIFFRACTION100
3.4127-3.67610.24371370.16562623X-RAY DIFFRACTION99
3.6761-4.0460.2011410.14692624X-RAY DIFFRACTION100
4.046-4.63120.17551450.13352652X-RAY DIFFRACTION100
4.6312-5.83380.17991390.14932661X-RAY DIFFRACTION100
5.8338-54.81710.16771330.15812708X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9045-0.59030.44112.2964-0.59112.55070.0329-0.0045-0.3335-0.2045-0.00280.47760.2316-0.04010.01060.1990.00660.03470.2673-0.00550.370811.2713-9.464841.4358
22.3918-0.3511-0.81321.23620.83711.7380.19920.04460.21980.2591-0.0007-0.14340.0613-0.1156-0.19520.43750.0898-0.06670.34240.02340.280331.5372-25.65321.7854
37.342-1.8666-1.00453.36660.72424.8362-0.0864-0.29870.25440.10450.09041.0794-0.4322-0.35650.01080.36610.10710.02590.31420.02810.6318-0.868916.036338.9406
43.2596-0.74751.36142.0613-2.37115.52670.1166-0.2187-0.33480.04870.047-0.22330.88450.321-0.13280.87890.1877-0.2230.4751-0.02550.41745.4973-49.83577.4651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 10:414)
2X-RAY DIFFRACTION2(chain B and resid 10:414)
3X-RAY DIFFRACTION3(chain C and resid 1:106)
4X-RAY DIFFRACTION4(chain D and resid 1:106)

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