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- PDB-2a15: X-ray Crystal Structure of RV0760 from Mycobacterium Tuberculosis... -

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Basic information

Entry
Database: PDB / ID: 2a15
TitleX-ray Crystal Structure of RV0760 from Mycobacterium Tuberculosis at 1.68 Angstrom Resolution
ComponentsHYPOTHETICAL PROTEIN Rv0760cHypothesis
KeywordsUNKNOWN FUNCTION / beta-alpha-barrel / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


sterol binding / isomerase activity / protein homodimerization activity
Similarity search - Function
Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE / Steroid isomerase, putative
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsGaren, C.R. / Cherney, M.M. / James, M.N.G. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Biochim.Biophys.Acta / Year: 2008
Title: Crystal structure of Mycobacterium tuberculosis Rv0760c at 1.50 A resolution, a structural homolog of Delta(5)-3-ketosteroid isomerase
Authors: Cherney, M.M. / Garen, C.R. / James, M.N.G.
History
DepositionJun 17, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN Rv0760c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3782
Polymers15,2561
Non-polymers1221
Water3,423190
1
A: HYPOTHETICAL PROTEIN Rv0760c
hetero molecules

A: HYPOTHETICAL PROTEIN Rv0760c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7564
Polymers30,5122
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area2550 Å2
ΔGint-0 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.600, 55.600, 104.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Cell settingtrigonal
Space group name H-MP3212
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: y-x,y,2/3-z

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Components

#1: Protein HYPOTHETICAL PROTEIN Rv0760c / Hypothesis


Mass: 15256.006 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SIMILARITY WITH PDB IDs 1BUQ, 1CQS, 1E3R, 1E3V, 1OH0 ETC. SUGGESTS THAT THIS PROTEIN IS KETOSTEROID ISOMERASE
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0760 / Production host: Escherichia coli (E. coli) / References: UniProt: P71817
#2: Chemical ChemComp-NCA / NICOTINAMIDE / Nicotinamide


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Comment: medication*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 M Na, K Phosphate, 100mM Hepes buffer pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.68→48.17 Å / Num. all: 21399 / Num. obs: 21399 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 7.6 % / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2refinement
SCALEPACKdata scaling
MOLREPphasing
ELVESrefinement
ELVESdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: the model was obtained from a SAD solution from the data collected on SeMet variant of the same protein.

Resolution: 1.68→48.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.813 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1076 5 %RANDOM
Rwork0.176 ---
all0.178 20320 --
obs0.178 20320 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.639 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.68→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1059 0 9 190 1258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221096
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.9261490
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4625132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.74124.11851
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82715178
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.906156
X-RAY DIFFRACTIONr_chiral_restr0.1350.2166
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02832
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2080.2517
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2744
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2148
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0253676
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.04341083
X-RAY DIFFRACTIONr_scbond_it6.5518477
X-RAY DIFFRACTIONr_scangle_it9.1110405
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.68→1.724 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 83 -
Rwork0.259 1469 -
obs--99.23 %

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