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- PDB-4tt5: Crystal Structure of CYP119 from Sulfolobus acidocaldarius, compl... -

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Basic information

Entry
Database: PDB / ID: 4tt5
TitleCrystal Structure of CYP119 from Sulfolobus acidocaldarius, complexed with 4-(4-bromophenyl)-1H imidazole
ComponentsCytochrome P450 119
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / peroxidase / lactoperoxidase activity / 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-bromophenyl)-1H-imidazole / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 119
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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.
History
DepositionJun 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._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 1.2Nov 27, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)43,8564
Polymers42,9241
Non-polymers9323
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.340, 165.340, 76.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-403-

GOL

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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


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-36Y / 4-(4-bromophenyl)-1H-imidazole


Mass: 223.069 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7BrN2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 3.53 Å3/Da / Density % sol: 65.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.85-1.2 Ammonium Sulfate 80mM Ammonium Acetate pH 4.5 20mM Ammonium Acetate pH 5.6 340mM NaCl 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 28, 2014
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.18→20 Å / Num. obs: 32672 / % possible obs: 99.8 % / Redundancy: 34.9 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 31.12
Reflection shellResolution: 2.18→2.3 Å / Redundancy: 24.4 % / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F4T

1f4t


Resolution: 2.18→19.857 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1587 4.86 %Random
Rwork0.1819 ---
obs0.1838 32665 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→19.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3018 0 61 200 3279
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093164
X-RAY DIFFRACTIONf_angle_d1.084287
X-RAY DIFFRACTIONf_dihedral_angle_d14.4251202
X-RAY DIFFRACTIONf_chiral_restr0.045462
X-RAY DIFFRACTIONf_plane_restr0.005545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.25030.29881560.23832760X-RAY DIFFRACTION100
2.2503-2.33060.28521380.22012782X-RAY DIFFRACTION100
2.3306-2.42370.30861400.21432780X-RAY DIFFRACTION100
2.4237-2.53380.24451350.21442799X-RAY DIFFRACTION100
2.5338-2.66710.27791220.2132790X-RAY DIFFRACTION100
2.6671-2.83380.24361440.22032797X-RAY DIFFRACTION100
2.8338-3.05180.24861540.21622806X-RAY DIFFRACTION100
3.0518-3.35760.23891450.20382816X-RAY DIFFRACTION100
3.3576-3.84040.23331450.17422851X-RAY DIFFRACTION100
3.8404-4.8270.18631470.14442880X-RAY DIFFRACTION100
4.827-19.8580.17651610.15863017X-RAY DIFFRACTION100

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