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- PDB-2v5l: Structures of the Open and Closed State of Trypanosomal Triosepho... -

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Basic information

Entry
Database: PDB / ID: 2v5l
TitleStructures of the Open and Closed State of Trypanosomal Triosephosphate Isomerase: as Observed in a New Crystal Form: Implications for the Reaction Mechanism
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsOXIDOREDUCTASE / TRIOSEPHOSPHATE ISOMERASE / PENTOSE SHUNT / GLUCONEOGENESIS / BINDING STUDIES / TIM / ISOMERASE / GLYCOSOME / GLYCOLYSIS / ENGINEERING / LIPID SYNTHESIS / FATTY ACID BIOSYNTHESIS
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
Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsNoble, M.E.M. / Zeelen, J.P. / Wierenga, R.K.
CitationJournal: Proteins: Struct.,Funct., Genet. / Year: 1993
Title: Structures of the Open and Closed State of Trypanosomal Triosephosphate Isomerase: As Observed in a New Crystal Form: Implications for the Reaction Mechanism
Authors: Noble, M.E.M. / Zeelen, J.P. / Wierenga, R.K.
History
DepositionJul 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9244
Polymers53,7322
Non-polymers1922
Water1,45981
1
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9244
Polymers53,7322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area3460 Å2
ΔGint-45.49 kcal/mol
Surface area19130 Å2
MethodPISA
2
B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules

B: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9244
Polymers53,7322
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3460 Å2
ΔGint-47.05 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.600, 48.200, 130.700
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE / / TRIOSE-PHOSPHATE ISOMERASE GLYCOSOMSAL / TIM


Mass: 26865.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN HOUSE NAME P4MAS_W3TB.PDB (RESIDUES 203 AND 503 ARE NOW AN ALANINE) RELATED PDB'S 1TPD AND 1TRD. ...IN HOUSE NAME P4MAS_W3TB.PDB (RESIDUES 203 AND 503 ARE NOW AN ALANINE) RELATED PDB'S 1TPD AND 1TRD. THIS IS AN OLD STRUCTURE THAT WAS ALREADY USED IN PUBLICATION NOBLE, M.E.M., ZEELEN, J.P., WIERENGA, R.K. (1993) PROTEINS, 16, 311-326. IN THAT ARTICLE IT WAS REFERRED WITH IN-HOUSE NAME P4MAS_W3TB.PDB. WE WANT TO DEPOSIT THIS STRUCTURE, BECAUSE SOME DETAILS OF IT HAVE BECOME RELEVANT FOR OUR FORTHCOMING PUBLICATION. ONLY THE COORDINATES AND THE INFORMATION ON THE ARTICLE FROM 1993 ARE AVAILABLE FOR US. THIS MEANS THAT MOST OF THE INFORMATION FOR THE HEADER FILES IS NOT AVAILABLE.

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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: 2.7 Å3/Da / Density % sol: 54.87 % / Description: NONE
Crystal growpH: 8.8
Details: 18% PEG6000, 200 MM TRIS PH 8.8, 1MM EDTA, 1MM DTT AND 1MM NAN3

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-21 / Wavelength: 1.5418
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. obs: 20429 / % possible obs: 81.8 % / Observed criterion σ(I): 99 / Redundancy: 1.95 % / Rmerge(I) obs: 0.05
Reflection shellResolution: 2.4→2.43 Å / % possible all: 41.8

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Processing

Software
NameVersionClassification
TNTNULLrefinement
XDSdata reduction
GRONINGENBIOMOL PACKAGEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 999 / Details: X-PLOR USED IN THE INITIAL STAGES OF REFINEMENT /
RfactorNum. reflection
Rwork0.158 -
obs0.158 39764
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 10 81 3857

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