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- PDB-2dp3: Crystal structure of a double mutant (C202A/A198V) of Triosephosp... -

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Basic information

Entry
Database: PDB / ID: 2dp3
TitleCrystal structure of a double mutant (C202A/A198V) of Triosephosphate isomerase from giardia lamblia
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TRIOSEPHOSPHATE ISOMERASE / GIARDIA / ENZYME / ALPHA/BETA BARREL
Function / homology
Function and homology information


methylglyoxal synthase / methylglyoxal synthase activity / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesGiardia intestinalis (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDiaz, A. / Reyes-Vivas, H. / Lopez-Velazquez, G.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Disulfide Bridges in the Mesophilic Triosephosphate Isomerase from Giardia lamblia Are Related to Oligomerization and Activity
Authors: Reyes-Vivas, H. / Diaz, A. / Peon, J. / Mendoza-Hernandez, G. / Hernandez-Alcantara, G. / De la Mora-De la Mora, I. / Enriquez-Flores, S. / Dominguez-Ramirez, L. / Lopez-Velazquez, G.
#1: Journal: Proteins / Year: 2004
Title: An unusual triosephosphate isomerase from the early divergent eukaryote Giardia lamblia
Authors: Lopez-Velazquez, G. / Molina-Ortiz, D. / Cabrera, N. / Peon-Peralta, J. / Reyes-Vivas, H.
History
DepositionMay 5, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 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 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)28,3205
Polymers27,9361
Non-polymers3844
Water5,459303
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,64110
Polymers55,8722
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
Buried area4440 Å2
ΔGint-118 kcal/mol
Surface area19520 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)55.371, 100.443, 118.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe second part of the biological assembly is generated by the two fold axis:

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Components

#1: Protein Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 27936.176 Da / Num. of mol.: 1 / Mutation: C202A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia intestinalis (eukaryote) / Strain: WB STRAIN / Gene: gltim / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: P36186, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.96 Å3/Da / Density % sol: 58.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 5microL of C202A (13mg/mL) dissolved in 100mM triethanolamine, 10mM EDTA, mixed with 5microL of 2M ammonium sulfate,5% isopropanol, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 11, 2004 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→28.65 Å / Num. obs: 18609 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.071
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.065 / Mean I/σ(I) obs: 8.1 / Num. unique all: 2875 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOSFLMdata reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1tcd, 1lyx, 1m6j

1tcd

1lyx

1m6j


Resolution: 2.1→28.65 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.181 955 RANDOM
Rwork0.175 --
all-19773 -
obs-18608 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.05 Å21.07 Å21.98 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati sigma a obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1939 0 20 303 2262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d1.74
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.009
RfactorNum. reflection% reflection
Rfree0.166 340 -
Rwork0.171 --
obs-2895 98.6 %

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