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- PDB-1ydv: TRIOSEPHOSPHATE ISOMERASE (TIM) -

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Basic information

Entry
Database: PDB / ID: 1ydv
TitleTRIOSEPHOSPHATE ISOMERASE (TIM)
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / GLYCOLYSIS / GLUCONEOGENESIS
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / identical protein binding / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVelankar, S.S. / Murthy, M.R.N.
Citation
Journal: Structure / Year: 1997
Title: Triosephosphate isomerase from Plasmodium falciparum: the crystal structure provides insights into antimalarial drug design.
Authors: Velanker, S.S. / Ray, S.S. / Gokhale, R.S. / Suma, S. / Balaram, H. / Balaram, P. / Murthy, M.R.
#1: Journal: Mol.Biochem.Parasitol. / Year: 1993
Title: Cloning of the Triosephosphate Isomerase Gene of Plasmodium Falciparum and Expression in Escherichia Coli
Authors: Ranie, J. / Kumar, V.P. / Balaram, H.
History
DepositionApr 24, 1997Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Apr 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: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)55,9952
Polymers55,9952
Non-polymers00
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-23 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.910, 47.640, 118.430
Angle α, β, γ (deg.)90.00, 108.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE / TIM


Mass: 27997.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Production host: Escherichia coli (E. coli) / References: UniProt: Q07412, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.55 Å3/Da / Density % sol: 48.01 %
Crystal growpH: 7.5
Details: 10 MG/ML PROTEIN IN 12% PEG 6000 IN HEPES BUFFER PH 7.5, 1MM DTT EQUILIBRATED AGAINST 24% PEG 6000 IN HEPES BUFFER PH 7.5, 1MM DTT
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
124 %(w/v)PEG60001reservoir
31 mMDTT1reservoir
412 %(w/v)PEG60001drop
60.5 mMDTT1drop
710 mg/mlprotein1drop
2HEPES1reservoir
5HEPES1drop

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: FRANCS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→15 Å / Num. obs: 25936 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.089
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.252 / % possible all: 83.9
Reflection
*PLUS
Num. measured all: 39357
Reflection shell
*PLUS
% possible obs: 83.9 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRYPANOSOMAL TIM

Resolution: 2.2→10 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: LYS A 12 AND LYS B 12 HAVE POSITIVE PHI ANGLE WHICH IS IMPORTANT FOR THE ACTIVITY OF THE PROTEIN.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 2497 10.2 %RANDOM
Rwork0.198 ---
obs0.198 24508 92 %-
Displacement parametersBiso mean: 14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 0 171 4085
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.351.5
X-RAY DIFFRACTIONx_mcangle_it3.362
X-RAY DIFFRACTIONx_scbond_it4.482
X-RAY DIFFRACTIONx_scangle_it6.62.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.312 219 9.8 %
Rwork0.25 2008 -
obs--83.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2WAT.PARWAT.TOP
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.28

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