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- PDB-1mss: LARGE SCALE STRUCTURAL REARRANGEMENTS OF THE FRONT LOOPS IN MONOM... -

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Basic information

Entry
Database: PDB / ID: 1mss
TitleLARGE SCALE STRUCTURAL REARRANGEMENTS OF THE FRONT LOOPS IN MONOMERISED TRIOSEPHOSPHATE ISOMERASE, AS DEDUCED FROM THE COMPARISON OF THE STRUCTURAL PROPERTIES OF MONOTIM AND ITS POINT MUTATION VARIANT MONOSS
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
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: Structure / Year: 1993
Title: The Crystal Structure of an Engineered Monomeric Triose Phosphate Isomerase, Monotim: The Correct Modelling of an Eight-Residue Loop
Authors: Borchert, T.V. / Abagyan, R. / Radha Kishan, K.V. / Zeelen, J.P. / Wierenga, R.K.
History
DepositionJul 27, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: 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 / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
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
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)52,0412
Polymers52,0412
Non-polymers00
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-8 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.570, 46.580, 66.650
Angle α, β, γ (deg.)94.47, 69.82, 75.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26020.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / References: UniProt: P04789, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE NO BREAKS IN THE PROTEIN CHAIN FOR EITHER OF THE MOLECULES BUT THERE IS A BREAK IN THE ...THERE ARE NO BREAKS IN THE PROTEIN CHAIN FOR EITHER OF THE MOLECULES BUT THERE IS A BREAK IN THE NUMBERING OF THE CHAINS. THIS IS DUE TO A LOOP DELETION MUTATION. RESIDUES 72 AND 80 ARE CONNECTED BY A PEPTIDE BOND. 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. PROTEIN DATA BANK ENTRY 1TRI PRESENTS STRUCTURE "MONOTIM"; THIS ENTRY PRESENTS STRUCTURE "MONOSS". THE DIFFERENCES BETWEEN MONOTIM AND MONOSS ARE F45S AND V46S. SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TPIS_TRYBB THE FOLLOWING RESIDUES ARE MISSING FROM THE N-TERMINUS OF CHAIN A AND CHAIN B. SEQUENCE NUMBER IS THAT FROM SWISS-PROT ENTRY. MET 1 SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE ARG 203 ALA 203 THE DISCREPANCY IS DUE TO THE CORRECT IDENTIFICATION IN THE DEPOSITOR'S LABORATORY AFTER TPIS_TRYBB HAD BEEN SUBMITTED. (BORCHERT ET AL., EUR. J. BIOCHEM., V211, 703, 1993). THIS ALANINE IS COMPLETELY CONSERVED IN ALL PUBLISHED TIM SEQUENCES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1drop
21 mMdithiothreitol1drop
31 mMEDTA1drop
41 mM1dropNaN3
55 %MPD1drop
610 %PEG80001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Num. obs: 13847 / % possible obs: 71 % / Num. measured all: 22787 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 20 %

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Processing

Software
NameClassification
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→24 Å /
RfactorNum. reflection
Rwork0.198 -
obs0.198 13620
Refinement stepCycle: LAST / Resolution: 2.4→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3642 0 0 56 3698
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_deg0.8
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

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