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- PDB-1ml1: PROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATE ISOMERASE: THE... -

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Basic information

Entry
Database: PDB / ID: 1ml1
TitlePROTEIN ENGINEERING WITH MONOMERIC TRIOSEPHOSPHATE ISOMERASE: THE MODELLING AND STRUCTURE VERIFICATION OF A SEVEN RESIDUE LOOP
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / COMPLEX (ISOMERASE-PHOSPHOGLYCOLIC ACID) / INTRAMOLECULAR OXIDOREDUCTASE / LOOP DESIGN
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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsThanki, N. / Zeelen, J.P. / Mathieu, M. / Jaenicke, R. / Abagyan, R.A. / Wierenga, R. / Schliebs, W.
Citation
Journal: Protein Eng. / Year: 1997
Title: Protein engineering with monomeric triosephosphate isomerase (monoTIM): the modelling and structure verification of a seven-residue loop.
Authors: Thanki, N. / Zeelen, J.P. / Mathieu, M. / Jaenicke, R. / Abagyan, R.A. / Wierenga, R.K. / Schliebs, W.
#1: Journal: Protein Sci. / Year: 1996
Title: Active Site Properties of Monomeric Triosephosphate Isomerase (Monotim) as Deduced from Mutational and Structural Studies
Authors: Schliebs, W. / Thanki, N. / Eritja, R. / Wierenga, R.
#2: 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.
#3: Journal: Structure / Year: 1993
Title: The Crystal Structure of an Engineered Monomeric Triosephosphate Isomerase, Monotim: The Correct Modelling of an Eight-Residue Loop
Authors: Borchert, T.V. / Abagyan, R. / Kishan, K.V.R. / Zeelen, J.P. / Wierenga, R.K.
History
DepositionSep 27, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_database_status / pdbx_initial_refinement_model / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
C: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
I: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,75812
Polymers156,8216
Non-polymers9366
Water95553
1
A: TRIOSEPHOSPHATE ISOMERASE
C: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5864
Polymers52,2742
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5864
Polymers52,2742
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: TRIOSEPHOSPHATE ISOMERASE
K: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5864
Polymers52,2742
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)165.230, 165.230, 51.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.481, -0.876, -0.042), (0.872, -0.483, 0.082), (-0.092, 0.003, 0.996)83.498, -44.294, 5.411
2given(-0.514, 0.858, -0.012), (-0.851, -0.507, 0.137), (0.111, 0.081, 0.991)80.238, 49.466, -5.066
3given(-0.997, 0.029, -0.073), (0.028, 0.999, 0.023), (0.074, 0.021, -0.997)80.417, 45.473, 21.125
4given(0.479, -0.878, -0.008), (-0.87, -0.476, 0.132), (-0.12, -0.056, -0.991)2.09, 97.357, 31.289
5given(0.492, 0.869, -0.053), (0.87, -0.492, 0.019), (-0.01, -0.055, -0.998)-3.24, 3.709, 25.264

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE / MONOTIM


Mass: 26136.889 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote) / Species: Trypanosoma brucei / Strain: brucei / Cell line: XL1-BLUE / Plasmid: BL21 / Species (production host): Escherichia coli / Cell line (production host): XL1-BLUE / 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.: 6
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.6 Å3/Da / Density % sol: 49 %
Crystal growpH: 7.5 / Details: PLEASE SEE JRNL ARTICLE, pH 7.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
210 mMTEA-HCl1drop
325 mM1dropNaCl
41 mMdithiothreitol1drop
51 mMEDTA1drop
61 mMsodium azide1drop
710 mM2PG1drop
9100 mMTris-HCl1reservoir
8reservoir solution1drop1 ml
101.0 M1reservoirLi2SO4
110.7 Mammonium sulphate1reservoir
121 mMdithiothreitol1reservoir
131 mMEDTA1reservoir
141 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.6→21 Å / Num. obs: 45363 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 12
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3 / % possible all: 96.2
Reflection
*PLUS
Num. measured all: 124266
Reflection shell
*PLUS
% possible obs: 96.2 % / Rmerge(I) obs: 0.297

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TTJ

1ttj


Resolution: 2.6→32 Å / Rfactor Rfree error: 0.53 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.247 2104 5 %RANDOM
Rwork0.231 ---
obs0.231 45363 94.6 %-
Refinement stepCycle: LAST / Resolution: 2.6→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10956 0 54 53 11063
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_deg1.61
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
LS refinement shellHighest resolution: 2.6 Å
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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