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

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Basic information

Entry
Database: PDB / ID: 1ttj
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 / glycolytic process / gluconeogenesis / cytoplasm / 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
PHOSPHOGLYCOLOHYDROXAMIC 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.
Citation
Journal: 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.
#1: Journal: To be Published
Title: The 2.4 Angstrom Crystal Structure of the Complex of Monoss (A Monomeric Variant of Trypanosomal Triosephosphate Isomerase) and a Transition State Analogue, Phosphoglycolohydroxamate
Authors: Radha Kishan, K.V. / Ph Zeelen, J. / Schliebs, W. / Wierenga, R.K.
History
DepositionApr 20, 1995Processing site: BNL
Revision 1.0Sep 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)26,1922
Polymers26,0211
Non-polymers1711
Water72140
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.060, 39.330, 68.320
Angle α, β, γ (deg.)90.00, 117.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26020.688 Da / Num. of mol.: 1
Mutation: VARIANT OF MONOTIM WITH PHE 45 REPLACED BY SER AND VAL 46 REPLACED BY SER (F45S, V46S) AND 73 - 79 DELETED
Source method: isolated from a natural source / Source: (natural) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE IS ONE BREAK IN THE SEQUENCE AT 73. RESIDUE NUMBERS 73 - 79 ARE MISSING DUE TO DELETION OF A ...THERE IS ONE BREAK IN THE SEQUENCE AT 73. RESIDUE NUMBERS 73 - 79 ARE MISSING DUE TO DELETION OF A LOOP FROM THE PARENT MODEL AND CONNECTING THE ENDS 72 - 80 BY MUTATION. THE MUTATIONS WITH RESPECT TO MONOTIM ARE F45S AND V46S.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal grow
*PLUS
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
515 mMPGH1drop
633 %PEG60001reservoir

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Data collection

ReflectionResolution: 2.4→32 Å / Num. obs: 8529 / % possible obs: 86 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 20243 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 74 %

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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-8529 86 %
Refinement stepCycle: LAST / Resolution: 2.4→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 10 40 1821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.69
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 / Rfactor Rwork: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.7

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