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- PDB-4wje: Crystal structure of Trichomonas vaginalis triosephosphate isomer... -

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Basic information

Entry
Database: PDB / ID: 4wje
TitleCrystal structure of Trichomonas vaginalis triosephosphate isomerase V45A at 1.3 Angstroms
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / isomerase glycolysis monomer mutant
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.285 Å
AuthorsJimenez-Sandoval, P. / Rojas-Mendez, K. / Lara-Gonzalez, S. / Brieba, L.G.
CitationJournal: To Be Published
Title: Crystal structure of Trichomonas vaginalis triosephosphate isomerase V45A at 1.3 Angstroms
Authors: Jimenez-Sandoval, P. / Rojas-Mendez, K. / Lara-Gonzalez, S. / Brieba, L.G.
History
DepositionSep 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Sep 27, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7352
Polymers27,7121
Non-polymers231
Water2,324129
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4704
Polymers55,4242
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3420 Å2
ΔGint-47 kcal/mol
Surface area17640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.642, 106.784, 47.095
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Triosephosphate isomerase


Mass: 27711.863 Da / Num. of mol.: 1 / Mutation: V45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_096350 / Variant: Val-45 variant / Plasmid: pET19B / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: A2FT29, triose-phosphate isomerase
#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


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.57 Å3/Da / Density % sol: 52.14 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.16 M NaOAc, 0.08 M Sodium cacodylate, 14.4% PEG, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.285→20.14 Å / Num. all: 73262 / Num. obs: 73090 / % possible obs: 99.8 % / Observed criterion σ(F): 1.34 / Redundancy: 7.7 % / Biso Wilson estimate: 9.51 Å2 / Rmerge(I) obs: 0.097 / Χ2: 1.573 / Net I/av σ(I): 29.674 / Net I/σ(I): 8.4 / Num. measured all: 562511
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.29-1.317.536111.623100
1.31-1.347.535871.5251000.874
1.34-1.367.536251.571000.728
1.36-1.397.536291.5791000.667
1.39-1.427.535921.511000.586
1.42-1.457.536201.5881000.511
1.45-1.497.536311.5421000.435
1.49-1.537.536361.631000.381
1.53-1.577.636461.4861000.311
1.57-1.637.636201.5421000.262
1.63-1.687.736311.4441000.214
1.68-1.757.736481.5321000.176
1.75-1.837.836571.4051000.14
1.83-1.937.736351.6811000.12
1.93-2.05836811.4861000.084
2.05-2.218.136651.5181000.068
2.21-2.438.336871.6321000.061
2.43-2.788.437371.5481000.052
2.78-3.58.237531.6491000.043
3.5-506.737992.01495.90.041

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.29 Å20.14 Å
Translation1.29 Å20.14 Å

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QST

3qst


Resolution: 1.285→20.138 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 3682 5.04 %Random selection
Rwork0.172 69338 --
obs0.1728 73020 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 40.7 Å2 / Biso mean: 11.2605 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: final / Resolution: 1.285→20.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 1 129 1971
Biso mean--9.42 18.88 -
Num. residues----250
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081925
X-RAY DIFFRACTIONf_angle_d1.2052628
X-RAY DIFFRACTIONf_chiral_restr0.048302
X-RAY DIFFRACTIONf_plane_restr0.007345
X-RAY DIFFRACTIONf_dihedral_angle_d11.426672
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.285-1.30190.25781330.2212307244088
1.3019-1.31980.23471380.225926822820100
1.3198-1.33860.23211420.217226442786100
1.3386-1.35860.22731500.205726122762100
1.3586-1.37980.19811440.198826672811100
1.3798-1.40240.21861300.19226392769100
1.4024-1.42660.20911650.185626522817100
1.4266-1.45260.19881350.180626562791100
1.4526-1.48050.18921500.174526492799100
1.4805-1.51070.16541370.168126552792100
1.5107-1.54350.19321280.166326492777100
1.5435-1.57940.20621310.157427062837100
1.5794-1.61890.18431360.155426892825100
1.6189-1.66270.14781320.150626492781100
1.6627-1.71160.17411410.160626752816100
1.7116-1.76680.17861350.157426732808100
1.7668-1.82990.1691460.157826832829100
1.8299-1.90310.17911450.158526582803100
1.9031-1.98960.15811410.158726942835100
1.9896-2.09440.17451330.157727032836100
2.0944-2.22550.18021640.158626832847100
2.2255-2.39710.15861330.165527122845100
2.3971-2.63780.18061410.176927392880100
2.6378-3.01840.21681460.174827232869100
3.0184-3.79870.17421590.17362697285698
3.7987-20.140.20841470.18242842298998

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