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- PDB-4jeq: Different Contribution of Conserved Amino Acids to the Global Pro... -

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Basic information

Entry
Database: PDB / ID: 4jeq
TitleDifferent Contribution of Conserved Amino Acids to the Global Properties of Homologous Enzymes
ComponentsTRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
KeywordsISOMERASE / TIM BARREL / DISEASE MUTATION / PENTOSE SHUNT / GLUCONEOGENESIS / GLYCOLYSIS
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 / 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
DI(HYDROXYETHYL)ETHER / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.303 Å
AuthorsHernandez-Santoyo, A. / Aguirre-Fuentes, Y. / Torres-Larios, A. / Gomez-Puyou, A. / De Gomez-Puyou, M.T.
CitationJournal: Proteins / Year: 2014
Title: Different contribution of conserved amino acids to the global properties of triosephosphate isomerases.
Authors: Aguirre, Y. / Cabrera, N. / Aguirre, B. / Perez-Montfort, R. / Hernandez-Santoyo, A. / Reyes-Vivas, H. / Enriquez-Flores, S. / de Gomez-Puyou, M.T. / Gomez-Puyou, A. / Sanchez-Ruiz, J.M. / Costas, M.
History
DepositionFeb 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
C: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
D: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
E: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
F: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
G: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
H: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
I: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
J: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
K: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
L: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,23322
Polymers322,22212
Non-polymers1,01110
Water10,701594
1
A: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1186
Polymers53,7042
Non-polymers4144
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-25 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
D: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0025
Polymers53,7042
Non-polymers2983
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-34 kcal/mol
Surface area19110 Å2
MethodPISA
3
E: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
F: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8103
Polymers53,7042
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-17 kcal/mol
Surface area19380 Å2
MethodPISA
4
G: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
H: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8003
Polymers53,7042
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-33 kcal/mol
Surface area18880 Å2
MethodPISA
5
I: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
J: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL


Theoretical massNumber of molelcules
Total (without water)53,7042
Polymers53,7042
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-31 kcal/mol
Surface area19220 Å2
MethodPISA
6
K: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
L: TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8003
Polymers53,7042
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-33 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.087, 89.782, 181.718
Angle α, β, γ (deg.)90.00, 101.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 26851.807 Da / Num. of mol.: 12 / Mutation: E104D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: MEXICAN NINOA / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 594 / 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: 2.18 Å3/Da / Density % sol: 43.69 %
Crystal growTemperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 25% w/v PEG monomethyl ether 2000, 0.1 M Tris, 0.01 M Nickel (II) chloride hexahydrate, 5% w/v n-dodecyl-N,N-dimethylamin-N-oxide , pH 8.6, VAPOR DIFFUSION, SITTING DROP, temperature 281.15K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9791 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 28, 2010
Details: HIGH-RESOLUTION DOUBLE- CRYSTAL SI(220) SAGITTAL FOCUSING, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→89.78 Å / Num. all: 122434 / Num. obs: 122434 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 36.51 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.086 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.303-2.329194
2.329-2.3561100
2.356-2.385199
2.385-2.4151100
2.415-2.4471100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1307)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J27

2j27


Resolution: 2.303→61.577 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 28.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2614 5914 5.03 %RANDOM
Rwork0.2071 ---
obs0.2099 122273 99.4 %-
all-122434 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.303→61.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22464 0 60 594 23118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00922913
X-RAY DIFFRACTIONf_angle_d1.12931056
X-RAY DIFFRACTIONf_dihedral_angle_d15.0058172
X-RAY DIFFRACTIONf_chiral_restr0.0723611
X-RAY DIFFRACTIONf_plane_restr0.0053948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.303-2.32920.33252150.25033657X-RAY DIFFRACTION94
2.3292-2.35660.32562230.24973783X-RAY DIFFRACTION100
2.3566-2.38530.29362030.23373891X-RAY DIFFRACTION99
2.3853-2.41550.27671990.21983822X-RAY DIFFRACTION100
2.4155-2.44730.30241820.21973875X-RAY DIFFRACTION100
2.4473-2.48080.30071950.23213884X-RAY DIFFRACTION100
2.4808-2.51630.32342000.26153849X-RAY DIFFRACTION99
2.5163-2.55380.28772130.22273829X-RAY DIFFRACTION100
2.5538-2.59370.31162150.21623889X-RAY DIFFRACTION100
2.5937-2.63630.29141980.23083895X-RAY DIFFRACTION100
2.6363-2.68170.35561950.26333848X-RAY DIFFRACTION99
2.6817-2.73050.29592310.22993856X-RAY DIFFRACTION100
2.7305-2.7830.32631990.24513855X-RAY DIFFRACTION100
2.783-2.83980.32472120.24733891X-RAY DIFFRACTION100
2.8398-2.90160.30551860.23613922X-RAY DIFFRACTION100
2.9016-2.96910.33211780.23263864X-RAY DIFFRACTION100
2.9691-3.04330.3242090.22943907X-RAY DIFFRACTION100
3.0433-3.12560.28841940.22763886X-RAY DIFFRACTION100
3.1256-3.21760.29682240.22733888X-RAY DIFFRACTION100
3.2176-3.32140.28942370.23263856X-RAY DIFFRACTION100
3.3214-3.44010.3091970.22683879X-RAY DIFFRACTION100
3.4401-3.57780.25032170.20983866X-RAY DIFFRACTION100
3.5778-3.74060.2372020.20013899X-RAY DIFFRACTION100
3.7406-3.93780.23272160.20413858X-RAY DIFFRACTION99
3.9378-4.18450.24192070.18723888X-RAY DIFFRACTION99
4.1845-4.50750.21041940.16923910X-RAY DIFFRACTION100
4.5075-4.96090.19692130.16543876X-RAY DIFFRACTION99
4.9609-5.67830.24321610.1823954X-RAY DIFFRACTION99
5.6783-7.15240.2492150.19093891X-RAY DIFFRACTION99
7.1524-61.59870.18572150.17533960X-RAY DIFFRACTION98

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