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- PDB-3qsr: Crystal structure of Trichomonas vaginalis triosephosphate isomer... -

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Basic information

Entry
Database: PDB / ID: 3qsr
TitleCrystal structure of Trichomonas vaginalis triosephosphate isomerase TVAG_497370 gene (Ile-45 variant)
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM barrel
Function / homology
Function and homology information


glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / 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 speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsLara-Gonzalez, S. / Salgado-Lugo, H. / Brieba, L.G.
CitationJournal: To be Published
Title: Crystal structure of Trichomonas vaginalis triosephosphate isomerase TVAG_497370 gene
Authors: Salgado-Lugo, H. / Lara-Gonzalez, S. / Brieba, L.G.
History
DepositionFeb 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source

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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)27,8342
Polymers27,8111
Non-polymers231
Water3,279182
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6684
Polymers55,6222
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565x,-y+1,-z1
Buried area3780 Å2
ΔGint-47 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.820, 55.750, 103.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-277-

HOH

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Components

#1: Protein Triosephosphate isomerase /


Mass: 27810.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_497370 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star rossetaII / References: UniProt: A2EGX9
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Calcium acetate; 0.1 M Sodium cacodylate; 18 % PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002+
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.05→38.014 Å / Num. all: 15748 / Num. obs: 15748 / % possible obs: 88.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.9 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 16.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.05-2.166.70.4331.71348520030.43379.4
2.16-2.296.60.3971.91230918520.39777.4
2.29-2.456.60.2433.11480122420.24399
2.45-2.656.60.1953.91392221080.19599.7
2.65-2.96.80.12861095416000.12881.6
2.9-3.247.20.0868.81273217730.08699.9
3.24-3.747.50.05813929412340.05877.9
3.74-4.587.60.04515.6917912120.04588.6
4.58-6.487.40.04513.7797310750.045100
6.48-38.0146.80.02723.743956490.02799.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 29.09 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å38.01 Å
Translation2.5 Å38.01 Å

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→35.853 Å / Occupancy max: 1 / Occupancy min: 0.37 / SU ML: 0.27 / Isotropic thermal model: Isotropic / σ(F): 0 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 999 6.36 %Random
Rwork0.1758 ---
obs0.1788 15712 88.72 %-
all-17710 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.198 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso max: 58.6 Å2 / Biso mean: 19.7753 Å2 / Biso min: 7.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.4747 Å2-0 Å20 Å2
2---1.5444 Å2-0 Å2
3---4.0191 Å2
Refinement stepCycle: LAST / Resolution: 2.05→35.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1887 0 1 182 2070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051925
X-RAY DIFFRACTIONf_angle_d0.9352614
X-RAY DIFFRACTIONf_chiral_restr0.066297
X-RAY DIFFRACTIONf_plane_restr0.004341
X-RAY DIFFRACTIONf_dihedral_angle_d14.218686
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.0501-2.15820.31281250.225518371962183779
2.1582-2.29330.291210.205117881909178878
2.2933-2.47040.25781580.172323142472231499
2.4704-2.71890.2261350.180519892124198985
2.7189-3.11210.23751610.18237325342373100
3.1121-3.92020.18921310.163719362067193685
3.9202-35.85890.1861680.1628247626442476100

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