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- PDB-1tti: THREE NEW CRYSTAL STRUCTURES OF POINT MUTATION VARIANTS OF MONOTI... -

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Basic information

Entry
Database: PDB / ID: 1tti
TitleTHREE NEW CRYSTAL STRUCTURES OF POINT MUTATION VARIANTS OF MONOTIM: CONFORMATIONAL FLEXIBILITY OF LOOP-1,LOOP-4 AND LOOP-8
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / cytosol / 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsRadha Kishan, K.V. / Wierenga, R.K.
CitationJournal: Structure / Year: 1995
Title: Three new crystal structures of point mutation variants of monoTIM: conformational flexibility of loop-1, loop-4 and loop-8.
Authors: Borchert, T.V. / Kishan, K.V. / Zeelen, J.P. / Schliebs, W. / Thanki, N. / Abagyan, R. / Jaenicke, R. / Wierenga, R.K.
History
DepositionApr 19, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Nov 3, 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 1.6Feb 14, 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)26,3502
Polymers26,1941
Non-polymers1561
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.780, 46.760, 70.390
Angle α, β, γ (deg.)90.00, 113.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26193.943 Da / Num. of mol.: 1 / Mutation: I68G, A69N, K70A, S71D, DEL(73-79), P81A, A100W
Source method: isolated from a genetically manipulated source
Details: MONOTIM WITH A110W MUTATION / Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei
Description: ESCHERICHIA COLI STRAIN XL1-BLUE USED FOR THE GENETIC MANIPULATIONS
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHERE IS ONE MOLECULE PER ASYMMETRIC UNIT. THERE IS ONE SUBSTRATE ANALOGUE, BOUND IN THE ACTIVE ...THERE IS ONE MOLECULE PER ASYMMETRIC UNIT. THERE IS ONE SUBSTRATE ANALOGUE, BOUND IN THE ACTIVE SITE. ITS RESIDUE NAME IS PGA: 2-PHOSPHOGLYCOLIC ACID.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.59 %
Crystal grow
*PLUS
Temperature: 20 R.T. / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES1drop
21 mMDTT1drop
31 mMEDTA1drop
41 mM1dropNaN3
53 mM2PG1drop
622 %PEG60001reservoir

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Data collection

ReflectionResolution: 2.4→32 Å / Num. obs: 7034 / % possible obs: 25 % / Observed criterion σ(I): 0
Reflection
*PLUS
% possible obs: 75 % / Num. measured all: 11293 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 25 %

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→32 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.178 --
obs-7034 75 %
Refinement stepCycle: LAST / Resolution: 2.4→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1794 0 9 12 1815
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.28
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Rfactor obs: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2.3

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