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- PDB-2whf: Interaction of Mycobacterium tuberculosis CYP130 with heterocycli... -

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Basic information

Entry
Database: PDB / ID: 2whf
TitleInteraction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines
ComponentsPUTATIVE CYTOCHROME P450 130
KeywordsOXIDOREDUCTASE / IRON / HEME / MONOOXYGENASE / METAL-BINDING / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


cholest-4-en-3-one 26-monooxygenase activity / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen / cell wall / steroid hydroxylase activity / cholesterol catabolic process / peptidoglycan-based cell wall / 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
PROTOPORPHYRIN IX CONTAINING FE / 1-(3-METHYLPHENYL)-1H-BENZIMIDAZOL-5-AMINE / Cytochrome P450 130 / Cytochrome P450 130
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsPodust, L.M. / Ouellet, H. / von Kries, J.P. / Ortiz de Montellano, P.R.
CitationJournal: J. Biol. Chem. / Year: 2009
Title: Interaction of Mycobacterium tuberculosis CYP130 with heterocyclic arylamines.
Authors: Podust, L.M. / Ouellet, H. / von Kries, J.P. / de Montellano, P.R.
History
DepositionMay 4, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary
Revision 1.2Feb 7, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 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 / 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 / _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

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Assembly

Deposited unit
A: PUTATIVE CYTOCHROME P450 130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7694
Polymers45,7061
Non-polymers1,0633
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)160.897, 53.942, 44.047
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PUTATIVE CYTOCHROME P450 130 / CYP130


Mass: 45705.566 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-405
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCWORI / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): HMS174
References: UniProt: Q11062, UniProt: P9WPN5*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen
#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-II4 / 1-(3-METHYLPHENYL)-1H-BENZIMIDAZOL-5-AMINE


Mass: 223.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H13N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Sequence details6 HIS-TAG RESIDUES ARE ADDED AT THE N-TERMINUS. A 406 SER AND A 407 ARG ARE INTRODUCED AT THE C- ...6 HIS-TAG RESIDUES ARE ADDED AT THE N-TERMINUS. A 406 SER AND A 407 ARG ARE INTRODUCED AT THE C-TERMINUS AS A RESULT OF GENERATING XBAI 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: 2.04 Å3/Da / Density % sol: 39.3 % / Description: NONE
Crystal growpH: 5.5
Details: 20% PEG 4000, 0.1M NA ACETATE, PH 5.5; 3% ISOPROPYL ALCOHOL

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 14, 2008 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 51244 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 39.7
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2UUQ

2uuq


Resolution: 1.58→79.81 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.117 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
RfactorNum. reflection% reflectionSelection details
Rfree0.23963 5131 10.1 %RANDOM
Rwork0.19556 ---
obs0.19999 45902 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.131 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å2-0.91 Å2
2---0.49 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.58→79.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 77 164 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213250
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6562.0084467
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1845410
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53322.302139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32915481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2571532
X-RAY DIFFRACTIONr_chiral_restr0.1050.2491
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212541
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3761.52004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.08223249
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.12831246
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.54.51213
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.93933250
X-RAY DIFFRACTIONr_sphericity_free8.3933164
X-RAY DIFFRACTIONr_sphericity_bonded5.93233155
LS refinement shellResolution: 1.581→1.622 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 379 -
Rwork0.229 3200 -
obs--95.64 %

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