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- PDB-2j27: The functional role of the conserved active site proline of trios... -

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Basic information

Entry
Database: PDB / ID: 2j27
TitleThe functional role of the conserved active site proline of triosephosphate isomerase
ComponentsTRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
KeywordsISOMERASE / TIM / 2PG / LOOP7 / GLYCOSOME / TIM-BARREL / GLUCONEOGENESIS / LIPID SYNTHESIS / ATOMIC RESOLUTION / GLYCOLYSIS / PENTOSE SHUNT / POINT MUTATION / FATTY ACID BIOSYNTHESIS / 2-PHOSPHO GLYCOLATE / PROTEIN ENGINEERING
Function / homology
Function and homology information


glycosome / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / cytoplasm
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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsCasteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2006
Title: Functional Role of the Conserved Active Site Proline of Triosephosphate Isomerase.
Authors: Casteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0885
Polymers53,6802
Non-polymers4083
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.810, 97.320, 112.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.724, -0.69), (0.024, -0.999, -0.025), (-0.689, -0.034, 0.724)
Vector: 1.31264, -0.03957, 0.21347)

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 26839.795 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 168 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 168 TO ALA

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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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growpH: 9.5
Details: WELL SOLUTION: 0.1 M CHES PH 9.5, 25 % PEG 1500, 200 MM MGSO4 PROTEIN SOLUTION: 11.5 MG/ML PROTEIN, 20 MM TRIS/HCL PH 7, 100 MM NACL, 1 MM DTT, 1 MM EDTA, 1 MM NAN3 AND 10 MM 2PG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9023
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2005 / Details: RH COATED, ZERODUR
RadiationMonochromator: FIXED EXIT DOUBLE CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9023 Å / Relative weight: 1
ReflectionResolution: 1.15→25 Å / Num. obs: 164758 / % possible obs: 92 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.12
Reflection shellResolution: 1.15→1.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.29 / % possible all: 76.3

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Processing

Software
NameClassification
SHELXL-97refinement
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIM

5tim


Resolution: 1.15→25 Å / Num. parameters: 40486 / Num. restraintsaints: 48408 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 8251 5 %RANDOM
obs0.1417 -91.8 %-
all-164768 --
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 17876
Refinement stepCycle: LAST / Resolution: 1.15→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 23 686 4469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0309
X-RAY DIFFRACTIONs_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.081

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