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- PDB-1if2: X-RAY STRUCTURE OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE ... -

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Basic information

Entry
Database: PDB / ID: 1if2
TitleX-RAY STRUCTURE OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE COMPLEXED WITH IPP
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / TIM barrel / transition state analogue
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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
[2(FORMYL-HYDROXY-AMINO)-ETHYL]-PHOSPHONIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKursula, I. / Partanen, S. / Lambeir, A.-M. / Antonov, D.M. / Augustyns, K. / Wierenga, R.K.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Structural determinants for ligand binding and catalysis of triosephosphate isomerase.
Authors: Kursula, I. / Partanen, S. / Lambeir, A.M. / Antonov, D.M. / Augustyns, K. / Wierenga, R.K.
History
DepositionApr 12, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3772
Polymers27,2081
Non-polymers1691
Water3,855214
1
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7554
Polymers54,4162
Non-polymers3382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3680 Å2
ΔGint-26 kcal/mol
Surface area19040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.234, 52.825, 58.937
Angle α, β, γ (deg.)90.00, 118.03, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE / E.C.5.3.1.1 / TIM


Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: E65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P48499, triose-phosphate isomerase
#2: Chemical ChemComp-129 / [2(FORMYL-HYDROXY-AMINO)-ETHYL]-PHOSPHONIC ACID


Mass: 169.073 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.5 Å3/Da / Density % sol: 50.89 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 6000, CH3COOH/NaOH, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
121 %PEG60001reservoir
2100 mM1reservoirpH4.5CH3COOH/NaOH
31 mMdithiothreitol1reservoirreduced
41 mMEDTA1reservoir
51 mMsodium azide1reservoir
611 mg/mlprotein1drop
710 mM2-phosphoglycolate1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 26, 2000 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 18318 / Num. obs: 18318 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.158 / Mean I/σ(I) obs: 9.3 / Num. unique all: 1843 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 74174
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.181 916 5 %random
Rwork0.16 ---
all0.136 18318 --
obs0.136 18318 --
Displacement parametersBiso mean: 22.2 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 10 214 2124
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d2.1
LS refinement shellResolution: 2→2.09 Å
RfactorNum. reflection% reflection
Rfree0.217 124 -
Rwork0.128 --
obs-2207 98.8 %
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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