[English] 日本語
Yorodumi
- PDB-1ypi: STRUCTURE OF YEAST TRIOSEPHOSPHATE ISOMERASE AT 1.9-ANGSTROMS RES... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ypi
TitleSTRUCTURE OF YEAST TRIOSEPHOSPHATE ISOMERASE AT 1.9-ANGSTROMS RESOLUTION
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)
Function / homology
Function and homology information


Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane ...Gluconeogenesis / Glycolysis / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / mitochondrion / plasma membrane / cytosol / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsAlber, T. / Lolis, E. / Petsko, G.A.
Citation
Journal: Biochemistry / Year: 1990
Title: Structure of yeast triosephosphate isomerase at 1.9-A resolution.
Authors: Lolis, E. / Alber, T. / Davenport, R.C. / Rose, D. / Hartman, F.C. / Petsko, G.A.
#1: Journal: Biochemistry / Year: 1990
Title: Crystallographic Analysis of the Complex between Triosephosphate Isomerase and 2-Phosphoglycolate at 2.5-Angstroms Resolution. Implications for Catalysis
Authors: Lolis, E. / Petsko, G.A.
#2: Journal: Cold Spring Harbor Symp.Quant.Biol. / Year: 1987
Title: Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a (Double Quote)Simple(Double Quote) Enzyme (Question Mark)
Authors: Alber, T.C. / Davenportjunior, R.C. / Giammona, D.A. / Lolis, E. / Petsko, G.A. / Ringe, D.
#3: Journal: J.Biol.Chem. / Year: 1981
Title: Crystallization of Yeast Triose Phosphate Isomerase from Polyethylene Glycol. Protein Crystal Formation Following Phase Separation
Authors: Alber, T. / Hartman, F.C. / Johnson, R.M. / Petsko, G.A. / Tsernoglou, D.
#4: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: On the Three-Dimensional Structure and Catalytic Mechanism of Triose Phosphate Isomerase
Authors: Alber, T. / Banner, D.W. / Bloomer, A.C. / Petsko, G.A. / Phillips, D. / Rivers, P.S. / Wilson, I.A.
History
DepositionJan 12, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Remark 700SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED ...SHEET THE SHEETS PRESENTED AS *BLA* AND *BLB* ON SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED BETA-BARRELS. THIS IS REPRESENTED BY A NINE-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)53,3922
Polymers53,3922
Non-polymers00
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-10 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.150, 98.550, 49.260
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: RESIDUES LYS A 12, ASN A 28, ASN A 35, HIS A 103, ARG B 3, HIS B 103, LEU B 131, ASP B 222 HAVE DIHEDRAL ANGLES THAT ARE SIGNIFICANTLY OUTSIDE THE RAMACHANDRAN LIMITS.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1.00004, -0.00217, -0.00079), (-0.0017, 0.43502, 0.90043), (-0.00226, 0.90281, -0.43581)
Vector: 120.42589, -12.98956, 20.80916)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*.

-
Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE


Mass: 26696.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P00942, triose-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERING IN EACH CHAIN IS SEQUENTIAL STARTING WITH 2.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.73 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion / Details: can also be done with bathch methods
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlyeast triosephosphate isomerase1reservoir
212 %satammonium sulfate1reservoir
31 mMEDTA1reservoir
41 mMmercaptoethanol1reservoir
550 mMTris-HCl1reservoir
616 %PEG40001reservoir

-
Data collection

Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 3 Å / Num. obs: 2028 / Rmerge(I) obs: 0.113

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.9→40 Å
Details: RESIDUES LYS A 12, ASN A 28, ASN A 35, HIS A 103, ARG B 3, HIS B 103, LEU B 131, ASP B 222 HAVE DIHEDRAL ANGLES THAT ARE SIGNIFICANTLY OUTSIDE THE RAMACHANDRAN LIMITS.
RfactorNum. reflection
obs0.21 35167
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3766 0 0 119 3885
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.03
X-RAY DIFFRACTIONp_angle_d0.0480.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.052
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: 1.9 Å / Lowest resolution: 40 Å / Num. reflection obs: 35167 / Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2.06 Å / Total num. of bins used: 7 / Num. reflection obs: 4880 / Rfactor obs: 0.253

+
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