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- PDB-1n55: 0.83A resolution structure of the E65Q mutant of Leishmania mexic... -

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Basic information

Entry
Database: PDB / ID: 1n55
Title0.83A resolution structure of the E65Q mutant of Leishmania mexicana triosephosphate isomerase complexed with 2-phosphoglycolate
Componentstriosephosphate isomerase
KeywordsISOMERASE / TIM / atomic resolution / enzyme-ligand complex / transition-state analogue / low-barrier hydrogen bond
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 / 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
ACETIC ACID / 2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.83 Å
AuthorsKursula, I. / Wierenga, R.K.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of triosephosphate isomerase complexed with 2-phosphoglycolate at 0.83-A resolution
Authors: Kursula, I. / Wierenga, R.K.
History
DepositionNov 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 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)27,7617
Polymers27,2081
Non-polymers5526
Water10,106561
1
A: triosephosphate isomerase
hetero molecules

A: triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,52114
Polymers54,4162
Non-polymers1,10512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5010 Å2
ΔGint-36 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.072, 50.580, 58.884
Angle α, β, γ (deg.)90.00, 118.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-801-

GOL

21A-1163-

HOH

31A-1332-

HOH

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Components

#1: Protein triosephosphate isomerase / TIM


Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: E65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / 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: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 6000, 0.1 M Na-acetate/NaOH, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Details: Kursula, I., (2001) Eur. J. Biochem., 268, 5189.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 %PEG60001reservoir
20.1 Macetic acid/NaOH1reservoirpH4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.84
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: Bent mirror
RadiationMonochromator: Triangular / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.84 Å / Relative weight: 1
ReflectionResolution: 0.83→25 Å / Num. all: 243382 / Num. obs: 241678 / % possible obs: 99.3 % / Redundancy: 4.3 % / Biso Wilson estimate: 6.88 Å2 / Rmerge(I) obs: 0.029 / Net I/σ(I): 34
Reflection shellResolution: 0.83→0.84 Å / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3 / % possible all: 97.2
Reflection
*PLUS
Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 97.2 % / Num. unique obs: 11796

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.83→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.1085 4859 random
Rwork0.0949 --
obs0.0949 236819 -
Refinement stepCycle: LAST / Resolution: 0.83→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 35 561 2496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.044
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.081
X-RAY DIFFRACTIONs_bond_d0.026
X-RAY DIFFRACTIONs_from_restr_planes0.441
X-RAY DIFFRACTIONs_approx_iso_adps0.11
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.1026
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_plane_restr / Dev ideal: 0.441

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