[English] 日本語
Yorodumi
- PDB-1mo0: Structural Genomics Of Caenorhabditis Elegans: Triose Phosphate I... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1mo0
TitleStructural Genomics Of Caenorhabditis Elegans: Triose Phosphate Isomerase
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / STRUCTURAL GENOMICS / Triose Phosphate Isomerase / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


Glycolysis / Gluconeogenesis / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / myofibril / cell redox homeostasis ...Glycolysis / Gluconeogenesis / methylglyoxal synthase / methylglyoxal synthase activity / triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / myofibril / cell redox homeostasis / glycolytic process / gluconeogenesis / determination of adult lifespan / 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
ACETATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAS / Resolution: 1.7 Å
AuthorsSymersky, J. / Li, S. / Finley, J. / Liu, Z.-J. / Qui, H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. ...Symersky, J. / Li, S. / Finley, J. / Liu, Z.-J. / Qui, H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. / Zhao, J. / Thomas, W. / Nagy, L.A. / Sha, B. / DeLucas, L.J. / Wang, B.-C. / Luo, M. / Southeast Collaboratory for Structural Genomics (SECSG)
Citation
Journal: Proteins / Year: 2003
Title: Structural genomics of Caenorhabditis elegans: triosephosphate isomerase
Authors: Symersky, J. / Li, S. / Carson, M. / Luo, M.
#1: Journal: To be published
Title: Structural genomics of Caenorhabditis elegans: The structure of the cytoskeleton-associated protein (CAP-Gly) domain of F53F4.3.
Authors: Li, S. / Finley, J. / Liu, Z.-J. / Qui, H. / Luan, C.H. / Carson, M. / Tsao, J. / Johnson, D. / Lin, G. / Zhao, J. / Thomas, W. / Nagy, L.A. / Sha, B. / DeLucas, L.J. / Wang, B.-C. / Luo, M.
History
DepositionSep 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3589
Polymers59,7602
Non-polymers5987
Water8,305461
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-96 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.399, 64.373, 105.706
Angle α, β, γ (deg.)90.00, 91.53, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

-
Components

#1: Protein Triosephosphate isomerase / E.C.5.3.1.1 / TIM


Mass: 29880.043 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Plasmid: PDEST 17.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q10657, triose-phosphate isomerase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.063 Å3/Da / Density % sol: 38.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2 M AMMONIUM SULFATE, 50 mM SODIUM ACETATE at pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Mammonium sulfate1reservoir
250 mMsodium acetate1reservoirpH5.5
316 mg/mlprotein1drop
415 mMHEPES1droppH7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.976
DetectorDetector: IMAGE PLATE / Date: Jun 22, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→29.6 Å / Num. all: 49911 / Num. obs: 49911 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Redundancy: 3.49 % / Biso Wilson estimate: 14.6 Å2 / Net I/σ(I): 15.1
Reflection shellResolution: 1.7→1.76 Å / % possible obs: 86.5 % / Redundancy: 2.64 % / Rsym value: 0.206
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 29.6 Å / Num. obs: 49994 / Num. measured all: 174695 / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Rmerge(I) obs: 0.206

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
RESOLVEmodel building
CNS1refinement
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAS
Starting model: THE STRUCTURE WAS SOLVED USING THE DATA COLLECTED ON R-AXIS IV WITH CU_KA RADIATION TO 2-A RESOLUTION. THE CRYSTAL WAS SOAKED WITH POTASSIUM IODIDE PRIOR DATA COLLECTION

Resolution: 1.7→29.6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2496 5 %RANDOM
Rwork0.183 ---
obs0.183 49911 92.6 %-
all-49911 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8849 Å2 / ksol: 0.384014 e/Å3
Displacement parametersBiso mean: 16.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å20 Å2-3.76 Å2
2---4.84 Å20 Å2
3---7.07 Å2
Refine analyzeLuzzati coordinate error free: 0.21 Å / Luzzati sigma a free: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3801 0 33 461 4295
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1441.5
X-RAY DIFFRACTIONc_mcangle_it1.8382
X-RAY DIFFRACTIONc_scbond_it1.6132
X-RAY DIFFRACTIONc_scangle_it2.5862.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 394 5 %
Rwork0.238 7413 -
obs--87.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ACT.PARAMACT.TOPOL
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 29.6 Å / Num. reflection obs: 49994 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

+
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