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- PDB-1tph: 1.8 ANGSTROMS CRYSTAL STRUCTURE OF WILD TYPE CHICKEN TRIOSEPHOSPH... -

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Basic information

Entry
Database: PDB / ID: 1tph
Title1.8 ANGSTROMS CRYSTAL STRUCTURE OF WILD TYPE CHICKEN TRIOSEPHOSPHATE ISOMERASE-PHOSPHOGLYCOLOHYDROXAMATE COMPLEX
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsTRIOSEPHOSPHATE ISOMERASE
Function / homology
Function and homology information


Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process ...Glycolysis / Glycolysis / Gluconeogenesis / Gluconeogenesis / methylglyoxal biosynthetic process / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / canonical glycolysis / glycolytic process / gluconeogenesis / ubiquitin protein ligase binding / protein homodimerization activity / 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
PHOSPHOGLYCOLOHYDROXAMIC ACID / Triosephosphate isomerase
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsZhang, Z. / Sugio, S. / Komives, E.A. / Liu, K.D. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
CitationJournal: Biochemistry / Year: 1994
Title: Crystal structure of recombinant chicken triosephosphate isomerase-phosphoglycolohydroxamate complex at 1.8-A resolution.
Authors: Zhang, Z. / Sugio, S. / Komives, E.A. / Liu, K.D. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
History
DepositionDec 22, 1993Processing site: BNL
Revision 1.0Apr 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: TRIOSEPHOSPHATE ISOMERASE
2: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4234
Polymers53,0812
Non-polymers3422
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-33 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.400, 74.000, 57.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26540.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00940, triose-phosphate isomerase
#2: Chemical ChemComp-PGH / PHOSPHOGLYCOLOHYDROXAMIC ACID


Mass: 171.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: TPIS_CHICK SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE SER 194 THR 194

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal grow
*PLUS
pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
3100 mMTris1reservoir
412.5-21.0 %(w/v)PEG80001reservoir
5200 mMlithium1reservoir
1phosphoglycolohydroxamate phosphate1dropsaturating amounts
2PEG1dropwide concentration

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 13 Å / Num. all: 52935 / Num. obs: 50153 / % possible obs: 95 %

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.8→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.185 47198
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 20 249 3981
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0340.035
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.7661
X-RAY DIFFRACTIONp_mcangle_it1.2271.5
X-RAY DIFFRACTIONp_scbond_it1.5321.5
X-RAY DIFFRACTIONp_scangle_it2.3272
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1250.13
X-RAY DIFFRACTIONp_singtor_nbd0.1830.4
X-RAY DIFFRACTIONp_multtor_nbd0.1850.4
X-RAY DIFFRACTIONp_xhyhbond_nbd0.170.4
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.33
X-RAY DIFFRACTIONp_staggered_tor15.815
X-RAY DIFFRACTIONp_orthonormal_tor34.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS

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