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- PDB-1f4t: THERMOPHILIC P450: CYP119 FROM SULFOLOBUS SOLFACTARICUS WITH 4-PH... -

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Basic information

Entry
Database: PDB / ID: 1f4t
TitleTHERMOPHILIC P450: CYP119 FROM SULFOLOBUS SOLFACTARICUS WITH 4-PHENYLIMIDAZOLE BOUND
ComponentsCYTOCHROME P450 119
KeywordsOXIDOREDUCTASE / P450 fold
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / lactoperoxidase activity / peroxidase / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol 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
PROTOPORPHYRIN IX CONTAINING FE / 4-PHENYL-1H-IMIDAZOLE / Cytochrome P450 119
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å
AuthorsYano, J.K. / Koo, L.S. / Schuller, D.J. / Li, H. / Ortiz de Montellano, P.R. / Poulos, T.L.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structure of a thermophilic cytochrome P450 from the archaeon Sulfolobus solfataricus.
Authors: Yano, J.K. / Koo, L.S. / Schuller, D.J. / Li, H. / Ortiz de Montellano, P.R. / Poulos, T.L.
History
DepositionJun 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 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_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.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_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: CYTOCHROME P450 119
B: CYTOCHROME P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6279
Polymers85,8482
Non-polymers1,7797
Water11,151619
1
A: CYTOCHROME P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8465
Polymers42,9241
Non-polymers9224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CYTOCHROME P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7814
Polymers42,9241
Non-polymers8573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-110 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.958, 114.600, 185.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME P450 119 / CYP119


Mass: 42924.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli)
References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one ...References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen into the other donor

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Non-polymers , 5 types, 626 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-PIM / 4-PHENYL-1H-IMIDAZOLE


Mass: 144.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG, EPPS, MgSO4, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
235 %PEG33501reservoir
3100 mMEPPS1reservoir
40.2 M1reservoirMgSO4
51 mM4-phenylimidazole1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength
SYNCHROTRONSSRL BL7-111.08
ROTATING ANODERIGAKU RU30021.54
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEJan 13, 2000
RIGAKU RAXIS IV2IMAGE PLATEJan 22, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
21.541
ReflectionResolution: 1.93→50 Å / Num. all: 61801 / Num. obs: 57793 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.03 % / Biso Wilson estimate: 22.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 24.1
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3 % / Rmerge(I) obs: 0.745 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.93→44.4 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3134779.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 2913 5 %RANDOM
Rwork0.225 ---
obs0.225 57793 93.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.13 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.36 Å20 Å20 Å2
2--3.45 Å20 Å2
3----10.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.93→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 119 619 6774
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 445 5.2 %
Rwork0.331 8099 -
obs--83.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2MYTOPPAR:PARAM.CNS.HETEROMYTOPPAR:TOPH.CNS.HETERO
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85

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