[English] 日本語
Yorodumi
- PDB-1tpc: OFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tpc
TitleOFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
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: 1.9 Å
AuthorsZhang, Z. / Sugio, S. / Komives, E.A. / Liu, K.D. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
Citation
Journal: Biochemistry / Year: 1995
Title: The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules.
Authors: Komives, E.A. / Lougheed, J.C. / Liu, K. / Sugio, S. / Zhang, Z. / Petsko, G.A. / Ringe, D.
#1: Journal: To be Published
Title: Offset of a Catalytic Lesion (Glu165Asp) of Triosephosphate Isomerase by Bound Waters Soluble
Authors: Zhang, Z. / Komives, E.A. / Sugio, S. / Liu, K.D. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
#2: Journal: To be Published
Title: Triosephosphate Isomerase Drinks Water to Keep Healthy
Authors: Zhang, Z. / Sugio, S. / Stock, A.M. / Komives, E.A. / Liu, K.D. / Narayana, N. / Huong, Ng.H. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
#3: Journal: To be Published
Title: The Structural Basis for Pseudoreversion of the E165D Lesion by the Secondary S96P Mutation in Triosephosphate Isomerase Depends on the Position of Bound Water Molecules
Authors: Komives, E.A. / Lougheed, J.C. / Zhang, Z. / Petsko, G.A. / Ringe, D.
#4: Journal: To be Published
Title: S96P Change is the Second-Site Suppressor for the H95N Sluggish Mutant Isomerase
Authors: Zhang, Z. / Sugio, S. / Komives, E.A. / Liu, K.D. / Stock, A.M. / Narayana, N. / Xuong, Ng.H. / Knowles, J.R. / Petsko, G.A. / Ringe, D.
#5: Journal: Biochemistry / Year: 1990
Title: How Can a Catalytic Lesion be Offset? the Energetics of Two Pseudorevertant Triosephosphate Isomerases
Authors: Blacklow, S.C. / Knowles, J.R.
History
DepositionFeb 3, 1994Processing site: BNL
Revision 1.0Feb 14, 1995Provider: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,4154
Polymers53,0732
Non-polymers3422
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-33 kcal/mol
Surface area18480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.400, 73.900, 55.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26536.301 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.: 234 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.64 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.5 MPGH1drop0.0048ml
3100 mMTris-HCl1reservoir
4200 mMlithium sulfate1reservoir
512.5-21 %PEG80001reservoirin 2.5% increments
2protein1drop0.1152ml

-
Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. obs: 37566 / % possible obs: 83 % / Num. measured all: 107422 / Rmerge(I) obs: 0.085

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→6 Å / σ(F): 1 /
RfactorNum. reflection
obs0.182 38793
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3712 0 20 234 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.015
X-RAY DIFFRACTIONp_angle_d0.030.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.042
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / Num. reflection obs: 28952 / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more