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- PDB-2y61: Crystal structure of Leishmanial E65Q-TIM complexed with S-Glycid... -

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Basic information

Entry
Database: PDB / ID: 2y61
TitleCrystal structure of Leishmanial E65Q-TIM complexed with S-Glycidol phosphate
ComponentsTRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM
KeywordsISOMERASE / FATTY ACID BIOSYNTHESIS / TRANSITION STATE ANALOGUE / GLYCOLYSIS / PENTOSE SHUNT / GLUCONEOGENESIS / ENZYME-LIGAND COMPLEX
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
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
SN-GLYCEROL-1-PHOSPHATE / SN-GLYCEROL-3-PHOSPHATE / Triosephosphate isomerase
Similarity search - Component
Biological speciesLEISHMANIA MEXICANA (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.99 Å
AuthorsVenkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K.
CitationJournal: Protein Sci. / Year: 2011
Title: High resolution crystal structures of triosephosphate isomerase complexed with its suicide inhibitors: the conformational flexibility of the catalytic glutamate in its closed, liganded active site.
Authors: Venkatesan, R. / Alahuhta, M. / Pihko, P.M. / Wierenga, R.K.
History
DepositionJan 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / diffrn_source / entity / exptl_crystal_grow
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_mutation / _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.1May 22, 2019Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_conn
Item: _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7375
Polymers27,2081
Non-polymers5284
Water7,512417
1
A: TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM
hetero molecules

A: TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,47310
Polymers54,4162
Non-polymers1,0578
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area3770 Å2
ΔGint-25.2 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.140, 52.470, 58.090
Angle α, β, γ (deg.)90.00, 117.85, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2253-

GOL

21A-3018-

HOH

31A-3416-

HOH

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE SYNONYM TRIOSE-PHOSPHATE ISOMERASE, TIM


Mass: 27208.236 Da / Num. of mol.: 1 / Mutation: E65Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LEISHMANIA MEXICANA (eukaryote) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): PLYSS / References: UniProt: P48499, triose-phosphate isomerase
#2: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#3: Chemical ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9O6P
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 66 TO GLN
Has protein modificationY
Nonpolymer details1G3P, GOP: MICROHETEROGENEITY OBSERVED. S-GLYCIDOL PHOSPHATE BECAME GLYCEROL PHOSPHATE ESTER WITH ...1G3P, GOP: MICROHETEROGENEITY OBSERVED. S-GLYCIDOL PHOSPHATE BECAME GLYCEROL PHOSPHATE ESTER WITH THE SIDECHAIN OXYGEN OF GLU1167.

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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: 2.3 Å3/Da / Density % sol: 0.48 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 21% PEG6000, 0.1 M SODIUM ACETATE PH 4.5-5.5, 1MM DTT, 1MM EDTA, 1MM NAN3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 0.8997
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8997 Å / Relative weight: 1
ReflectionResolution: 0.99→10 Å / Num. obs: 140160 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 21.4
Reflection shellResolution: 0.99→1.02 Å / Redundancy: 4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.8 / % possible all: 95.3

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N55

1n55


Resolution: 0.99→10 Å / Num. parameters: 22147 / Num. restraintsaints: 27895 / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1247 7003 5 %RANDOM
obs0.1057 -97.7 %-
all-133049 --
Refine analyzeOccupancy sum hydrogen: 1941.65 / Occupancy sum non hydrogen: 2322.88
Refinement stepCycle: LAST / Resolution: 0.99→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1900 0 30 417 2347
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol0.102
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.105
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.096
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.037
X-RAY DIFFRACTIONs_approx_iso_adps0.089

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