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- PDB-4wpd: X-ray Crystal Structure of CYP119 complexed with 4-(4-flouropheny... -

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Basic information

Entry
Database: PDB / ID: 4wpd
TitleX-ray Crystal Structure of CYP119 complexed with 4-(4-flourophenyl)-1H-imidazole
ComponentsCytochrome P450 119
KeywordsOXIDOREDUCTASE / Cytochrome P450 / 4-(4-flourophenyl)-1H-imidazole ligand bound
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
4-(4-fluorophenyl)-1H-imidazole / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 119
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.001 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: TWO DIMENTIONAL NMR AND X-RAY ANALYSIS OF CYP119 LIGAND DEPENDENT CONFORMATIONAL DYNAMICS
Authors: Basudhar, D. / Madrona, Y. / Kandel, S. / Lampe, J.N. / Ortiz de Montellano, P.
History
DepositionOct 17, 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 / 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 / pdbx_validate_close_contact
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 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_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)87,4056
Polymers85,8482
Non-polymers1,5574
Water14,106783
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-61 kcal/mol
Surface area30040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.801, 95.458, 106.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cytochrome P450 119 / Peroxidase


Mass: 42924.027 Da / Num. of mol.: 2
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 / Plasmid: PcWori / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 alpha
References: UniProt: Q55080, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen, peroxidase
#2: Chemical ChemComp-3SQ / 4-(4-fluorophenyl)-1H-imidazole


Mass: 162.164 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H7FN2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 783 / 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: 2.34 Å3/Da / Density % sol: 47.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: Well solution contained: 2% PEG 8K, 400 mM MgCl2 and 100 mM LiCl2 Additive contained: 1.4 ammonium sulfate, 80 mM sodium acetate, pH 4.5, 20 mM sodium acetate pH 5.6, 20% glycerol, and 200 mM NaCl
PH range: 4.5-5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 2→38.1 Å / Num. obs: 54418 / % possible obs: 99.1 % / Redundancy: 3.7 % / Net I/σ(I): 15.5
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4 / % possible all: 96.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.9_1692) / Classification: refinement
RefinementResolution: 2.001→36.42 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.9 / Phase error: 18.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1991 2000 3.68 %
Rwork0.1569 --
obs0.1584 54418 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→36.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6036 0 110 783 6929
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0376340
X-RAY DIFFRACTIONf_angle_d1.0368600
X-RAY DIFFRACTIONf_dihedral_angle_d13.4522407
X-RAY DIFFRACTIONf_chiral_restr0.042929
X-RAY DIFFRACTIONf_plane_restr0.0051094
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.02670.24931300.20373447X-RAY DIFFRACTION92
2.0267-2.05340.21921390.19523603X-RAY DIFFRACTION98
2.0534-2.08150.27641370.19333622X-RAY DIFFRACTION97
2.0815-2.11120.20091390.18733681X-RAY DIFFRACTION97
2.1112-2.14270.26571370.18263641X-RAY DIFFRACTION97
2.1427-2.17620.21351400.17623657X-RAY DIFFRACTION97
2.1762-2.21190.26121380.18163629X-RAY DIFFRACTION98
2.2119-2.250.20451420.17733622X-RAY DIFFRACTION97
2.25-2.29090.25741430.17013652X-RAY DIFFRACTION98
2.2909-2.3350.24291410.16853682X-RAY DIFFRACTION97
2.335-2.38260.19131420.16153609X-RAY DIFFRACTION97
2.3826-2.43440.19421420.15623655X-RAY DIFFRACTION98
2.4344-2.4910.21771350.15883638X-RAY DIFFRACTION98
2.491-2.55330.17851450.1573673X-RAY DIFFRACTION97
2.5533-2.62230.24661380.163657X-RAY DIFFRACTION98
2.6223-2.69950.24021420.15353703X-RAY DIFFRACTION98
2.6995-2.78660.20611380.15953633X-RAY DIFFRACTION98
2.7866-2.88610.2321370.1643722X-RAY DIFFRACTION98
2.8861-3.00160.25291410.15783659X-RAY DIFFRACTION98
3.0016-3.13820.18011410.16293668X-RAY DIFFRACTION98
3.1382-3.30350.20971440.15543647X-RAY DIFFRACTION98
3.3035-3.51030.19451420.14773657X-RAY DIFFRACTION98
3.5103-3.78110.15571340.13193707X-RAY DIFFRACTION98
3.7811-4.16110.15041420.12673680X-RAY DIFFRACTION98
4.1611-4.76210.14241450.13053682X-RAY DIFFRACTION98
4.7621-5.99550.18691380.14973657X-RAY DIFFRACTION98
5.9955-36.42610.15821390.15593689X-RAY DIFFRACTION99

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