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- PDB-4tuv: X-ray crystal structure of CYP119 from Sulfolobus acidocaldarius,... -

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Basic information

Entry
Database: PDB / ID: 4tuv
TitleX-ray crystal structure of CYP119 from Sulfolobus acidocaldarius, complexed with 4-(4-chlorophenyl)imidazole
ComponentsCytochrome P450 119
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / lactoperoxidase activity / peroxidase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / 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
4-(4-CHLOROPHENYL)IMIDAZOLE / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 119
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.501 Å
AuthorsMadrona, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: NMR and X-ray Analysis of CYP119 Ligand Dependent Conformational Changes.
Authors: Basudhar, D. / Madrona, Y. / Ortiz De Montellano, P.R.
History
DepositionJun 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_close_contact
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytochrome P450 119
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7193
Polymers42,9241
Non-polymers7952
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.800, 165.800, 75.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Cytochrome P450 119 / Peroxidase


Mass: 42924.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Strain: ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770
Gene: cyp119, Saci_2081 / Production host: Escherichia coli (E. coli)
References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen, peroxidase
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CPZ / 4-(4-CHLOROPHENYL)IMIDAZOLE


Mass: 178.618 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7ClN2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 1.1-1.5M Ammonium sulfate, 80mM sodium acetate pH 4.5, 20mM sodium acetate pH 5.6, 20% glycerol, 340mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127092 Å / Relative weight: 1
ReflectionResolution: 2.5→36.67 Å / Num. obs: 21711 / % possible obs: 99.9 % / Redundancy: 12.4 % / Net I/σ(I): 24.48

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.501→36.67 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2391 1108 5.1 %
Rwork0.1878 --
obs0.1903 21708 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.501→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 54 66 3138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013158
X-RAY DIFFRACTIONf_angle_d1.2124278
X-RAY DIFFRACTIONf_dihedral_angle_d16.081196
X-RAY DIFFRACTIONf_chiral_restr0.047462
X-RAY DIFFRACTIONf_plane_restr0.005545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.501-2.6150.33631200.26782527X-RAY DIFFRACTION100
2.615-2.75280.33111470.23862504X-RAY DIFFRACTION100
2.7528-2.92520.29071450.2422524X-RAY DIFFRACTION100
2.9252-3.1510.28471370.22222538X-RAY DIFFRACTION100
3.151-3.46790.2491480.20462542X-RAY DIFFRACTION100
3.4679-3.96920.24381550.18042562X-RAY DIFFRACTION100
3.9692-4.99870.15851290.15092621X-RAY DIFFRACTION100
4.9987-36.6760.23941270.17212782X-RAY DIFFRACTION100

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