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- PDB-3tao: Structure of Mycobacterium tuberculosis triosephosphate isomerase... -

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Basic information

Entry
Database: PDB / ID: 3tao
TitleStructure of Mycobacterium tuberculosis triosephosphate isomerase bound to phosphoglycolohydroxamate
ComponentsTriosephosphate isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / extracellular region / plasma membrane / cytosol
Similarity search - Function
Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel ...Triosephosphate isomerase, bacterial/eukaryotic / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHOGLYCOLOHYDROXAMIC ACID / Triosephosphate isomerase / Triosephosphate isomerase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsConnor, S.E. / Capodagli, G.C. / Deaton, M.K. / Pegan, S.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural and functional characterization of Mycobacterium tuberculosis triosephosphate isomerase.
Authors: Connor, S.E. / Capodagli, G.C. / Deaton, M.K. / Pegan, S.D.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8684
Polymers56,5262
Non-polymers3422
Water15,205844
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-33 kcal/mol
Surface area19580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.026, 55.736, 76.941
Angle α, β, γ (deg.)90.000, 104.030, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 28262.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: MT1482, MTCY493.16c, Rv1438, tpi, tpiA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P66940, UniProt: P9WG43*PLUS, triose-phosphate isomerase
#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16% PEG3350, 250 mM ammonium citrate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.978 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2010
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.45→74.65 Å / Num. all: 97577 / Num. obs: 94064 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.45→1.48 Å / % possible all: 86.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.77 Å
Translation2.5 Å42.77 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→28.882 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1904 / WRfactor Rwork: 0.1688 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8974 / SU B: 0.92 / SU ML: 0.037 / SU R Cruickshank DPI: 0.0644 / SU Rfree: 0.0646 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1835 4702 5 %RANDOM
Rwork0.1612 89362 --
obs0.1624 94064 96.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 107.91 Å2 / Biso mean: 16.6868 Å2 / Biso min: 4.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.34 Å2
2--0.79 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.45→28.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 20 844 4667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214224
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9525795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.73323.955177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57815654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4941527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2665
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213280
X-RAY DIFFRACTIONr_mcbond_it0.6931.52744
X-RAY DIFFRACTIONr_mcangle_it1.25324407
X-RAY DIFFRACTIONr_scbond_it1.99431480
X-RAY DIFFRACTIONr_scangle_it3.2434.51376
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 304 -
Rwork0.209 6054 -
all-6358 -
obs--88.43 %

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