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- PDB-3q37: Identification of Amino Acids that Account for Long-Range Interac... -

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Basic information

Entry
Database: PDB / ID: 3q37
TitleIdentification of Amino Acids that Account for Long-Range Interactions in Proteins Using Two Triosephosphate Isomerases from Pathogenic Trypanosomes.
ComponentsTIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein
KeywordsISOMERASE / TIM barrel
Function / homology
Function and homology information


glycosome / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / 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 / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
Trypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsGarcia-Torres, I. / Cabrera, N. / Torres-Larios, A. / Rodriguez-Bolanos, M. / Gomez-Puyou, A. / Perez-Montfort, R.
CitationJournal: Plos One / Year: 2011
Title: Identification of amino acids that account for long-range interactions in two triosephosphate isomerases from pathogenic trypanosomes.
Authors: Garcia-Torres, I. / Cabrera, N. / Torres-Larios, A. / Rodriguez-Bolanos, M. / Diaz-Mazariegos, S. / Gomez-Puyou, A. / Perez-Montfort, R.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein
B: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein
C: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein
D: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein


Theoretical massNumber of molelcules
Total (without water)109,2894
Polymers109,2894
Non-polymers00
Water17,781987
1
A: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein
B: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein


Theoretical massNumber of molelcules
Total (without water)54,6442
Polymers54,6442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-22 kcal/mol
Surface area19010 Å2
MethodPISA
2
C: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein
D: TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein


Theoretical massNumber of molelcules
Total (without water)54,6442
Polymers54,6442
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-23 kcal/mol
Surface area19300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.594, 77.258, 85.387
Angle α, β, γ (deg.)90.00, 116.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TIM from Trypanosoma cruzi/ TIM from Trypanosoma brucei brucei chimera protein / TIM / Triose-phosphate isomerase


Mass: 27322.244 Da / Num. of mol.: 4
Fragment: UNP P04789 residues 2-35 and 92-119, UNP P52270 residues 35-92 and 121-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (eukaryote), (gene. exp.) Trypanosoma cruzi (eukaryote)
Gene: TIM / Plasmid: pET3b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P04789, UniProt: P52270, triose-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 987 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 Sodium malonate, 20% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 9, 2008 / Details: mirrors
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.65→54.31 Å / Num. all: 107171 / Num. obs: 107171 / % possible obs: 91.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.3 / Redundancy: 3.1 % / Biso Wilson estimate: 13.4 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.073 / Net I/σ(I): 10.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.65-1.732.90.3383.9139030.27582.4
1.74-1.833.10.2375.3151950.19494.6
1.84-1.963.10.1717.1143920.1495.1
1.97-2.123.10.1219.6133650.09994.9
2.13-2.323.20.09711.3122440.0894.4
2.33-2.63.20.0812.6110250.06694
2.61-33.20.07114.796680.05993.2
3.01-3.683.30.06918.780580.05891.6
3.69-5.213.30.06120.861320.05189.9
5.223.40.05218.831890.04383.7

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Processing

Software
NameClassification
MAR345data collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCD

1tcd


Resolution: 1.65→41.75 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2204 5412 -random
Rwork0.1889 ---
all0.1905 116767 --
obs0.1905 107157 91.77 %-
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.65→41.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7540 0 0 987 8527
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg1.005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.65-1.70.30734660.2546X-RAY DIFFRACTION843177
1.7-1.770.2745600.2307X-RAY DIFFRACTION1034093
1.77-1.850.24095870.1949X-RAY DIFFRACTION1047695
1.85-1.950.245450.1818X-RAY DIFFRACTION1048895
1.95-2.070.21465360.1791X-RAY DIFFRACTION1048995
2.07-2.230.20975710.1802X-RAY DIFFRACTION1047295
2.23-2.460.21065180.173X-RAY DIFFRACTION1048994
2.46-2.820.2075130.1803X-RAY DIFFRACTION1048994
2.82-3.550.21635740.1896X-RAY DIFFRACTION1039892
3.55-41.760.2045420.1908X-RAY DIFFRACTION1026688

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