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- PDB-1qds: SUPERSTABLE E65Q MUTANT OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE IS... -

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Basic information

Entry
Database: PDB / ID: 1qds
TitleSUPERSTABLE E65Q MUTANT OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE (TIM)
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / TIM / LEISHMANIA / STABILITY / MUTAGENESIS / PKA
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
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
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLambeir, A.M. / Backmann, J. / Ruiz-Sanz, J. / Filimonov, V. / Nielsen, J.E. / Vriend, G. / Kursula, I. / Norledge, B.V. / Wierenga, R.K.
Citation
Journal: Eur.J.Biochem. / Year: 2000
Title: The ionization of a buried glutamic acid is thermodynamically linked to the stability of Leishmania mexicana triose phosphate isomerase.
Authors: Lambeir, A.M. / Backmann, J. / Ruiz-Sanz, J. / Filimonov, V. / Nielsen, J.E. / Kursula, I. / Norledge, B.V. / Wierenga, R.K.
#1: Journal: Protein Eng. / Year: 1999
Title: Structural and Mutagenesis Studies of Leishmania Triosephosphate Isomerase: a Point Mutation Can Convert a Mesophilic Enzyme into a Superstable Enzyme without Losing Catalytic Power
Authors: Williams, J.C. / Zeelen, J.P. / Neubauer, G. / Vriend, G. / Backmann, J. / Michels, P.A.M. / Lambeir, A.-M. / Wierenga, R.
History
DepositionJul 10, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Experimental preparation / Category: citation_author / exptl_crystal_grow / Item: _citation_author.name / _exptl_crystal_grow.temp
Revision 1.4Nov 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 1.5Feb 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)27,3642
Polymers27,2081
Non-polymers1561
Water2,252125
1
A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7294
Polymers54,4162
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3690 Å2
ΔGint-32 kcal/mol
Surface area19210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.260, 52.790, 58.880
Angle α, β, γ (deg.)90.00, 118.09, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: E65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / Plasmid: PET 3A / Production host: Escherichia coli (E. coli) / References: UniProt: P48499, 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.: 125 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 16 % PEG 6000 10 MM PGA, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %PEG60001reservoir
21 mMEDTA1reservoir
31 mMdithiothreitol1reservoir
41 mM1reservoirNaN3
5100 mMacetic acid/NaOH1reservoir
610 mM2-phosphoglycolate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 22, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 17304 / Num. obs: 98464 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 11.7
Reflection shellResolution: 2→2.06 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.169 / % possible all: 41.4
Reflection
*PLUS
Num. obs: 17304 / Num. measured all: 98464
Reflection shell
*PLUS
% possible obs: 41.4 %

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: PROTEIN (CCP4)
RfactorNum. reflection% reflectionSelection details
Rfree0.195 882 -RANDOM
Rwork0.153 ---
all-16406 --
obs-17304 94.8 %-
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 9 125 2040
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.04

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