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- PDB-4jx1: Crystal structure of reduced Cytochrome P450cam-putidaredoxin com... -

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Basic information

Entry
Database: PDB / ID: 4jx1
TitleCrystal structure of reduced Cytochrome P450cam-putidaredoxin complex bound to camphor and 5-exo-hydroxycamphor
Components
  • Camphor 5-monooxygenase
  • Putidaredoxin
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / reduced 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 / cytoplasm
Similarity search - Function
Adrenodoxin, iron-sulphur binding site / Adrenodoxin family, iron-sulfur binding region signature. / Adrenodoxin / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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 / 2Fe-2S iron-sulfur cluster binding domain / Beta-grasp 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 / 5-EXO-HYDROXYCAMPHOR / CAMPHOR / 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: 2.087 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 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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
E: Camphor 5-monooxygenase
F: Camphor 5-monooxygenase
G: Putidaredoxin
H: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,55828
Polymers235,8358
Non-polymers4,72320
Water35,0931948
1
A: Camphor 5-monooxygenase
C: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1127
Polymers58,9592
Non-polymers1,1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Camphor 5-monooxygenase
D: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9436
Polymers58,9592
Non-polymers9854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Camphor 5-monooxygenase
G: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3928
Polymers58,9592
Non-polymers1,4336
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
F: Camphor 5-monooxygenase
H: Putidaredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1127
Polymers58,9592
Non-polymers1,1535
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.850, 108.960, 115.160
Angle α, β, γ (deg.)90.00, 109.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules ABEFCDGH

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


Mass: 46597.715 Da / Num. of mol.: 4 / 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: 12360.977 Da / Num. of mol.: 4 / Mutation: C85S, C73S, D19C
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 , 7 types, 1968 molecules

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


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CAM / CAMPHOR / Camphor


Mass: 152.233 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16O
#5: Chemical ChemComp-CAH / 5-EXO-HYDROXYCAMPHOR


Mass: 168.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16O2
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Chemical
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe2S2
#8: Chemical ChemComp-1N0 / 1,1'-hexane-1,6-diyldipyrrolidine-2,5-dione / bis(maleimido)hexane, bound form


Mass: 280.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N2O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1948 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
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: SSRL / Beamline: BL7-1 / Wavelength: 1.09 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 2.087→57.2 Å / Num. obs: 118774 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 15.3
Reflection shellResolution: 2.087→2.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 7.9 / Rsym value: 0.159 / % possible all: 98.3

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Processing

Software
NameVersionClassification
Blu-IceIcedata 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: 2.087→44.87 Å / SU ML: 0.2 / σ(F): 1.37 / Phase error: 19.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2121 5959 5.02 %
Rwork0.1438 --
obs0.1472 118733 98.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.087→44.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15972 0 292 1948 18212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01216694
X-RAY DIFFRACTIONf_angle_d1.51922787
X-RAY DIFFRACTIONf_dihedral_angle_d14.2256171
X-RAY DIFFRACTIONf_chiral_restr0.082487
X-RAY DIFFRACTIONf_plane_restr0.0072987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.087-2.11070.24632050.15353600X-RAY DIFFRACTION96
2.1107-2.13550.21182100.13943785X-RAY DIFFRACTION99
2.1355-2.16160.21851800.13783748X-RAY DIFFRACTION99
2.1616-2.18890.23341870.13773760X-RAY DIFFRACTION99
2.1889-2.21770.23462120.13113762X-RAY DIFFRACTION99
2.2177-2.24810.18431720.12653753X-RAY DIFFRACTION99
2.2481-2.28020.2132020.12953762X-RAY DIFFRACTION99
2.2802-2.31430.22131870.13153733X-RAY DIFFRACTION99
2.3143-2.35040.20841890.13443800X-RAY DIFFRACTION99
2.3504-2.3890.23381890.13193754X-RAY DIFFRACTION99
2.389-2.43020.22652040.13383747X-RAY DIFFRACTION99
2.4302-2.47430.21541960.1343788X-RAY DIFFRACTION99
2.4743-2.52190.21341870.1423743X-RAY DIFFRACTION99
2.5219-2.57340.24271960.14673794X-RAY DIFFRACTION99
2.5734-2.62930.24731960.14613781X-RAY DIFFRACTION99
2.6293-2.69050.22782100.1493729X-RAY DIFFRACTION99
2.6905-2.75780.21652250.14123743X-RAY DIFFRACTION99
2.7578-2.83230.22312140.14243786X-RAY DIFFRACTION99
2.8323-2.91570.22791970.14793762X-RAY DIFFRACTION99
2.9157-3.00980.22062090.14653769X-RAY DIFFRACTION99
3.0098-3.11730.22232150.15143778X-RAY DIFFRACTION99
3.1173-3.24210.22082230.1593763X-RAY DIFFRACTION99
3.2421-3.38960.22992010.14713744X-RAY DIFFRACTION99
3.3896-3.56820.19272020.14413761X-RAY DIFFRACTION99
3.5682-3.79170.20171940.13993813X-RAY DIFFRACTION99
3.7917-4.08420.19292020.14463772X-RAY DIFFRACTION99
4.0842-4.49490.17211930.12773799X-RAY DIFFRACTION99
4.4949-5.14450.18481950.13313751X-RAY DIFFRACTION97
5.1445-6.47850.22861690.16813598X-RAY DIFFRACTION93
6.4785-44.88080.18881980.17483896X-RAY DIFFRACTION99
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)
10.7629-0.10260.1460.7972-0.01721.02170.03480.00440.0523-0.0813-0.0632-0.0364-0.0269-0.02080.0280.1182-0.0060.02170.0920.01020.1017-86.83377.41693.4382
21.55170.1905-0.11190.71740.01260.880.0394-0.1541-0.15640.0797-0.05150.05240.0669-0.15920.00860.1333-0.0138-0.01260.18760.05250.1545-43.716723.2803-4.0589
32.07170.3625-0.49732.761-1.15162.57920.0951-0.2385-0.19640.1419-0.12150.12010.2397-0.08090.04890.1875-0.04790.0260.14980.03270.141-88.6907-17.965616.6109
41.9261-0.60730.542.9987-0.89373.5485-0.14150.14870.3808-0.1335-0.02370.1007-0.3631-0.04220.15370.18520.0046-0.05380.19870.06360.2352-45.528648.2172-17.8351
51.0151-0.2653-0.12180.7653-0.05610.9104-0.0265-0.01750.03660.04180.0234-0.0083-0.0388-0.03580.00350.13110.0040.01850.09630.00110.0933-105.39286.096658.5827
60.82890.21960.16640.69890.20110.9235-0.0121-0.0118-0.034-0.0052-0.04030.00290.05440.01180.05560.11290.0098-0.0030.11540.0150.1201-62.021321.498750.9564
72.80190.8177-0.27593.21340.09443.8986-0.0008-0.1002-0.25310.09960.03190.1140.1642-0.1439-0.02110.12590.0180.00820.1330.04310.1679-107.787-20.359368.9855
81.6198-0.68580.90.41-0.45972.1126-0.14640.32710.4352-0.53470.24790.4846-0.393-0.2085-0.02880.4235-0.0475-0.15730.25880.12620.3892-64.268746.406336.9462
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)
5X-RAY DIFFRACTION5(chain E and resid 10:414)
6X-RAY DIFFRACTION6(chain F and resid 10:414)
7X-RAY DIFFRACTION7(chain G and resid 1:106)
8X-RAY DIFFRACTION8(chain H and resid 1:106)

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