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- PDB-2z77: X-ray crystal structure of RV0760c from Mycobacterium tuberculosi... -

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Basic information

Entry
Database: PDB / ID: 2z77
TitleX-ray crystal structure of RV0760c from Mycobacterium tuberculosis in complex with estradiol-17beta-hemisuccinate
ComponentsPutative steroid isomerase
KeywordsISOMERASE / alpha+beta conical barrel / complex with estradiol-17beta-hemisuccinate / Structural Genomics / 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 (NTF2) domain / Nuclear transport factor 2 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
ACETATE ION / Chem-HE7 / NICOTINAMIDE / Steroid isomerase, putative
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsCherney, M.M. / Garen, C.R. / 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.
History
DepositionAug 16, 2007Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 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 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative steroid isomerase
B: Putative steroid isomerase
C: Putative steroid isomerase
D: Putative steroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,38210
Polymers61,0244
Non-polymers1,3586
Water6,395355
1
A: Putative steroid isomerase
B: Putative steroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3165
Polymers30,5122
Non-polymers8043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
MethodPISA
2
C: Putative steroid isomerase
D: Putative steroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0665
Polymers30,5122
Non-polymers5543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
MethodPISA
4
A: Putative steroid isomerase
B: Putative steroid isomerase
hetero molecules

C: Putative steroid isomerase
D: Putative steroid isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,38210
Polymers61,0244
Non-polymers1,3586
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area5000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.906, 66.428, 80.303
Angle α, β, γ (deg.)90.00, 105.95, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTwo molecules in the asymmetric unit is a biological assembly

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Components

#1: Protein
Putative steroid isomerase


Mass: 15256.006 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv0760c, MT0785 / Plasmid: pGST-0760c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P71817
#2: Chemical ChemComp-HE7 / 4-{[(14beta,17alpha)-3-hydroxyestra-1,3,5(10)-trien-17-yl]oxy}-4-oxobutanoic acid / 1,3,5(10)-Estratrien-3-[(17beta)-diol]-17-hemisuccinate / (17beta-Estradiol)-17-hemisuccinate


Mass: 372.455 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C22H28O5 / Comment: medication, hormone*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NCA / NICOTINAMIDE


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


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 8% PEG 8000, 0.1M Sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 35166 / Num. obs: 35166 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Rsym value: 0.045 / Net I/σ(I): 17.09
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 2.04 / Rsym value: 0.426 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A15

2a15


Resolution: 2.03→36.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.617 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27713 1740 4.9 %RANDOM
Rwork0.20333 ---
obs0.20702 33416 95.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.926 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20.2 Å2
2---0.03 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.03→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4051 0 98 355 4504
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214264
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8311.9545798
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9925523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0824.145193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33815660
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7771524
X-RAY DIFFRACTIONr_chiral_restr0.1330.2644
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023248
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.21926
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22816
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2318
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.277
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.67522697
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49234205
X-RAY DIFFRACTIONr_scbond_it2.39531810
X-RAY DIFFRACTIONr_scangle_it3.27541593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 106 -
Rwork0.275 2396 -
obs--92.6 %

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