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- PDB-4x22: Crystal structure of Leptospira Interrogans Triosephosphate Isome... -

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Basic information

Entry
Database: PDB / ID: 4x22
TitleCrystal structure of Leptospira Interrogans Triosephosphate Isomerase (LiTIM)
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM BARRELS / BETA-ALPHA BARRELS
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 speciesLeptospira interrogans serovar Icterohaemorrhagiae str. RGA (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.084 Å
AuthorsPareek, V. / Balaram, P. / Murthy, M.R.N.
Funding support India, 1items
OrganizationGrant numberCountry
department of Biotechnology India
CitationJournal: Chembiochem / Year: 2016
Title: Connecting Active-Site Loop Conformations and Catalysis in Triosephosphate Isomerase: Insights from a Rare Variation at Residue 96 in the Plasmodial Enzyme
Authors: Pareek, V. / Samanta, M. / Joshi, N.V. / Balaram, H. / Murthy, M.R.N. / Balaram, P.
History
DepositionNov 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 9, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)27,6386
Polymers27,2691
Non-polymers3685
Water3,963220
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,27512
Polymers54,5392
Non-polymers73710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4860 Å2
ΔGint-5 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.020, 103.020, 66.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-540-

HOH

21A-569-

HOH

31A-587-

HOH

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Components

#1: Protein Triosephosphate isomerase / / TIM / Triose-phosphate isomerase


Mass: 27269.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira interrogans serovar Icterohaemorrhagiae str. RGA (bacteria)
Strain: RGA / Gene: LEP2GSC113_RS0110880 / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): AA200
References: UniProt: Q8F5I5*PLUS, triose-phosphate isomerase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000 / 2-(2-Methoxyethoxy)ethanol


Mass: 120.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe reference sequence database derived from str. RGA does not currently exist.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.71 Å3/Da / Density % sol: 66.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PEG6000, calcium chloride, EDTA, HEPES buffer, Sodium azide
PH range: 7-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.084→44.61 Å / Num. obs: 23354 / % possible obs: 95.9 % / Redundancy: 8.9 % / Net I/σ(I): 25.9
Reflection shellResolution: 2.08→6.59 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.9 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.084→44.61 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 2.616 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19101 1194 5.1 %RANDOM
Rwork0.15462 ---
obs0.1565 22141 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.395 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.084→44.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 24 221 2116
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191926
X-RAY DIFFRACTIONr_bond_other_d0.0010.021842
X-RAY DIFFRACTIONr_angle_refined_deg1.8921.9672590
X-RAY DIFFRACTIONr_angle_other_deg0.91634244
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3772574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32415329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.348157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022167
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02417
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9992.079997
X-RAY DIFFRACTIONr_mcbond_other1.9852.078996
X-RAY DIFFRACTIONr_mcangle_it2.8253.1041245
X-RAY DIFFRACTIONr_mcangle_other2.8273.1041246
X-RAY DIFFRACTIONr_scbond_it2.8932.326928
X-RAY DIFFRACTIONr_scbond_other2.8912.329929
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2833.3551345
X-RAY DIFFRACTIONr_long_range_B_refined6.02917.5752274
X-RAY DIFFRACTIONr_long_range_B_other5.70817.0552187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.084→2.138 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2 96 -
Rwork0.179 1622 -
obs--94.92 %

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