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- PDB-2uvn: Crystal structure of econazole-bound CYP130 from Mycobacterium tu... -

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Basic information

Entry
Database: PDB / ID: 2uvn
TitleCrystal structure of econazole-bound CYP130 from Mycobacterium tuberculosis
ComponentsCYTOCHROME P450 130
KeywordsOXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cholest-4-en-3-one 26-monooxygenase activity / cholesterol catabolic process / cell wall / steroid hydroxylase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / peptidoglycan-based cell wall / monooxygenase activity / iron ion binding / heme binding
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
Chem-ECN / FLUORIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome P450 130 / Cytochrome P450 130
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPodust, L.M. / Ortiz de Montellano, P.R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Mycobacterium Tuberculosis Cyp130: Crystal Structure, Biophysical Characterization, and Interactions with Antifungal Azole Drugs
Authors: Ouellet, H. / Podust, L.M. / Ortiz de Montellano, P.R.
History
DepositionMar 12, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Atomic model / Version format compliance
Revision 1.2Aug 1, 2012Group: Non-polymer description / Refinement description
Revision 1.3Feb 7, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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_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_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 130
B: CYTOCHROME P450 130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,32024
Polymers91,6742
Non-polymers2,64722
Water1,38777
1
A: CYTOCHROME P450 130
B: CYTOCHROME P450 130
hetero molecules

A: CYTOCHROME P450 130
B: CYTOCHROME P450 130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,64048
Polymers183,3474
Non-polymers5,29344
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area23350 Å2
ΔGint-297.8 kcal/mol
Surface area54850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.676, 130.676, 229.357
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.79352, -0.52541, -0.30702), (-0.54314, -0.83903, 0.03204), (-0.27444, 0.14133, -0.95116)
Vector: 4.79132)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME P450 130 / CYP130


Mass: 45836.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCWORI / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q11062, UniProt: P9WPN5*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen

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Non-polymers , 5 types, 99 molecules

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


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-ECN / 1-[(2S)-2-[(4-CHLOROBENZYL)OXY]-2-(2,4-DICHLOROPHENYL)ETHYL]-1H-IMIDAZOLE / S-Econazole


Mass: 381.684 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15Cl3N2O
#4: Chemical
ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: F
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details6XHIS-TAG AT THE N-TERMINUS SER 406 AND R 407 ARE INTRODUCED AT THE C-TERMINUS AS A RESULT OF ...6XHIS-TAG AT THE N-TERMINUS SER 406 AND R 407 ARE INTRODUCED AT THE C-TERMINUS AS A RESULT OF GENERATING A RESTRICTION SITE

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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: 5.65 Å3/Da / Density % sol: 78 % / Description: NONE
Crystal growpH: 6.25
Details: 1.4 M AMMONIUM SULFATE, 0.1 M MES, PH 6.25, 40 MM NAF

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 26, 2007 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 45935 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 29.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUQ

2uuq


Resolution: 3→49.67 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 40310.97 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: BULK SOLVENT MODEL USED. DISORDERED REGIONS WERE OMITTED FROM THE CRYSTAL STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.234 4204 10.1 %RANDOM
Rwork0.2 ---
obs0.2 41548 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.2059 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 64.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.56 Å20 Å20 Å2
2--9.56 Å20 Å2
3----19.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.55 Å
Refinement stepCycle: LAST / Resolution: 3→49.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6119 0 168 77 6364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.02
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it2.082
X-RAY DIFFRACTIONc_scbond_it1.682
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 609 10.3 %
Rwork0.322 5321 -
obs--78.1 %

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