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- PDB-2uuq: Crystal structure of CYP130 from Mycobacterium tuberculosis in th... -

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Basic information

Entry
Database: PDB / ID: 2uuq
TitleCrystal structure of CYP130 from Mycobacterium tuberculosis in the ligand-free form
ComponentsCYTOCHROME P450 130
KeywordsOXIDOREDUCTASE / P450 / IRON / HEME / MONOOXYGENASE / METAL-BINDING / HYPOTHETICAL PROTEIN
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 / cell wall / steroid hydroxylase activity / cholesterol catabolic process / 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
PROTOPORPHYRIN IX CONTAINING FE / ISOPROPYL ALCOHOL / Cytochrome P450 130 / Cytochrome P450 130
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.46 Å
AuthorsPodust, L.M. / Ortiz de Montellano, P.R.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Mycobacterium Tuberculosis Cyp130:Crystal 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 7, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3Feb 7, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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: CYTOCHROME P450 130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6946
Polymers45,8371
Non-polymers8575
Water5,278293
1
A: CYTOCHROME P450 130
hetero molecules

A: CYTOCHROME P450 130
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,38712
Polymers91,6742
Non-polymers1,71410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2090 Å2
ΔGint-17.4 kcal/mol
Surface area38010 Å2
MethodPQS
Unit cell
Length a, b, c (Å)160.005, 53.854, 43.726
Angle α, β, γ (deg.)90.00, 96.49, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CYTOCHROME P450 130 / CYP130


Mass: 45836.758 Da / Num. of mol.: 1
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
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-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Sequence details6 HIS-TAG RESIDUES ARE ADDED AT THE N-TERMINUS. TWO RESIDUES A 406 SER AND A 407 ARG ARE INTRODUCED ...6 HIS-TAG RESIDUES ARE ADDED AT THE N-TERMINUS. TWO RESIDUES A 406 SER AND A 407 ARG ARE INTRODUCED AT THE C- TERMINUS AS A RESULT OF GENERATING XBAI 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: 2.08 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growpH: 5.2
Details: 1.6 M AMMONIUM SULFATE, 0.1 M SODIUM CITRATE, PH=5.2, 2 % ISOPROPANOL

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 19-ID11.11587
SYNCHROTRONALS 8.3.120.97970, 0.96863
Detector
TypeIDDetectorDateDetails
ADSC CCD1CCDJul 2, 2007MIRRORS
ADSC CCD2CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI (111) DOUBLE CRYSTALMADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.115871
20.97971
30.968631
ReflectionResolution: 1.46→50 Å / Num. obs: 64293 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 46.4
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 6.5 / % possible all: 81.9

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.46→79.56 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.687 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.227 6225 10.1 %RANDOM
Rwork0.196 ---
obs0.199 55263 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.62 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-1.26 Å2
2---0.61 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.46→79.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3029 0 59 293 3381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223256
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9984476
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8525420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46222.657143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09915489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1771531
X-RAY DIFFRACTIONr_chiral_restr0.0810.2495
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022562
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21667
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22261
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2239
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.266
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9631.52065
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.41423289
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9331330
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9964.51176
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 407 -
Rwork0.212 3670 -
obs--87.04 %

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