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- PDB-1ag1: MONOHYDROGEN PHOSPHATE BINDING TO TRYPANOSOMAL TRIOSEPHOSPHATE IS... -

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Basic information

Entry
Database: PDB / ID: 1ag1
TitleMONOHYDROGEN PHOSPHATE BINDING TO TRYPANOSOMAL TRIOSEPHOSPHATE ISOMERASE
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) / ISOMERASE (INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
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
PHOSPHATE ION / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsVerlinde, C.L.M.J. / Hol, W.G.J.
CitationJournal: Eur.J.Biochem. / Year: 1991
Title: Anion binding at the active site of trypanosomal triosephosphate isomerase. Monohydrogen phosphate does not mimic sulphate.
Authors: Verlinde, C.L. / Noble, M.E. / Kalk, K.H. / Groendijk, H. / Wierenga, R.K. / Hol, W.G.
History
DepositionMar 28, 1997Processing site: BNL
Revision 1.0Jun 16, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: 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
O: TRIOSEPHOSPHATE ISOMERASE
T: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8273
Polymers53,7322
Non-polymers951
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-29 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.840, 97.600, 46.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE /


Mass: 26865.832 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei (eukaryote) / Organelle: GLYCOSOME / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.39 Å3/Da / Density % sol: 48.59 %
Crystal growpH: 7
Details: 2.4 M AMMONIUM SULFATE IN 0.2 MOPS BUFFER, PH 7.0 FOLLOWED BY TRANSFER TO 44% PEG-6000 CONTAINING 15 MM PHOSPHATE
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop / Details: Wierenga, R.K., (1984) J. Mol. Biol., 178, 487.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14.5 mg/mltriosephosphate isomerase1drop
260 %ammonium sulfate1drop
31 mMEDTA1drop
40.2 MMOPS1drop
51 mMdithiothreitol1drop
61 mMsodium azide1drop
760 %ammonium sulphate1reservoir
80.9 Mammonium sulphate1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Mar 1, 1990 / Details: STANDARD
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.36 Å / Num. obs: 17592 / % possible obs: 87.5 % / Observed criterion σ(I): 2 / Redundancy: 1.7 % / Rmerge(I) obs: 0.063

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Processing

Software
NameVersionClassification
ISOMORPHOUS- NO NEED FOR SOFTWAREmodel building
TNT5Crefinement
MADNESdata reduction
BIOMOLdata scaling
ISOMORPHOUSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6TIM

6tim


Resolution: 2.36→6 Å / Isotropic thermal model: TNT BCORREL V1.0 / Cross valid method: A POSTERIORI / σ(F): 3 / Stereochemistry target values: TNT PROTGEO /
RfactorNum. reflection
Rwork0.15 -
obs-17592
Refinement stepCycle: LAST / Resolution: 2.36→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 5 156 3927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg3
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5C / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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