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- PDB-3th6: Crystal structure of Triosephosphate isomerase from Rhipicephalus... -

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Basic information

Entry
Database: PDB / ID: 3th6
TitleCrystal structure of Triosephosphate isomerase from Rhipicephalus (Boophilus) microplus.
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / ALPHA/BETA BARREL / EMBRYOGENESIS / GLYCOLYSIS
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / 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 speciesRhipicephalus microplus (southern cattle tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsArreola, R. / Rodriguez-Romero, A. / Moraes, J. / Gomez-Puyou, A. / Perez-Montfort, R. / Logullo, C.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2011
Title: Structural and biochemical characterization of a recombinant triosephosphate isomerase from Rhipicephalus (Boophilus) microplus.
Authors: Moraes, J. / Arreola, R. / Cabrera, N. / Saramago, L. / Freitas, D. / Masuda, A. / da Silva Vaz, I. / Tuena de Gomez-Puyou, M. / Perez-Montfort, R. / Gomez-Puyou, A. / Logullo, C.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 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
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
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)54,2282
Polymers54,2282
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.384, 53.384, 278.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Triosephosphate isomerase


Mass: 27114.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Total RNA was isolated from 10-day-old eggs
Source: (gene. exp.) Rhipicephalus microplus (southern cattle tick)
Strain: Porto Alegre / Gene: TIM / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: A8B3A8, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES/Na, 1.4 M Trisodium citrate dihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.977 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→46.474 Å / Num. all: 17583 / Num. obs: 17583 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value
2.4-2.538.70.37522232925620.375
2.53-2.688.70.2742.22097624240.274
2.68-2.878.70.1941953222570.19
2.87-3.18.50.1395.21798621270.139
3.1-3.398.40.0977.11640419480.097
3.39-3.798.30.0777.91465117730.077
3.79-4.388.30.0715.81294115600.071
4.38-5.378.50.0796.81128613260.079
5.37-7.598.80.0648.9905110230.064

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.46 Å
Translation2.5 Å46.46 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASER1.3.2phasing
CNS1.2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WYI

1wyi


Resolution: 2.4→46.46 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 1907544 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED THE FOLLOWING RESIDUES ARE DISORDERED AND IT WERE NOT MODELED DUE TO POOR/NULL ELECTRON DENSITY. CHAIN A/B RESIDUES: MET1 AND ALA2. CHAIN A RESIDUES FROM LOOP6: ...Details: BULK SOLVENT MODEL USED THE FOLLOWING RESIDUES ARE DISORDERED AND IT WERE NOT MODELED DUE TO POOR/NULL ELECTRON DENSITY. CHAIN A/B RESIDUES: MET1 AND ALA2. CHAIN A RESIDUES FROM LOOP6: THR172, GLY173 AND LYS174. CHAIN B RESIDUES FROM LOOP6: GLY171 THR172, GLY173, LYS174 AND THR175. CHAIN B RESIDUE: GLY249
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1773 10.1 %RANDOM
Rwork0.186 ---
obs0.221 17481 99.9 %-
all-17583 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5156 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 80.29 Å2 / Biso mean: 29.8919 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å20 Å2
2--3.82 Å20 Å2
3----7.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 0 112 3828
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 285 9.7 %
Rwork0.238 2640 -
all-2925 -
obs-2640 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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