[English] 日本語
Yorodumi
- PDB-1hg3: Crystal structure of tetrameric TIM from Pyrococcus woesei. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1hg3
TitleCrystal structure of tetrameric TIM from Pyrococcus woesei.
ComponentsTRIOSEPHOSPHATE ISOMERASE
KeywordsISOMERASE / THERMOSTABILITY / PYROCOCCUS / TRIOSEPHOSPHATE ISOMERASE / TETRAMERIC
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / cytoplasm / cytosol
Similarity search - Function
Triosephosphate isomerase, archaeal / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / Triosephosphate isomerase, active site / Triosephosphate isomerase active site. / Triosephosphate isomerase / Triosephosphate isomerase superfamily / Triosephosphate isomerase / Triosephosphate isomerase (TIM) family profile. / Aldolase class I ...Triosephosphate isomerase, archaeal / Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / 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
3-PHOSPHONOPROPANOIC ACID / Triosephosphate isomerase / Triosephosphate isomerase
Similarity search - Component
Biological speciesPYROCOCCUS WOESEI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsWalden, H. / Bell, G.S. / Russell, R.J.M. / Siebers, B. / Hensel, R. / Taylor, G.L.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Tiny Tim: A Small, Tetrameric, Hyperthermostable Triosephosphate Isomerase
Authors: Walden, H. / Bell, G.S. / Russell, R.J.M. / Siebers, B. / Hensel, R. / Taylor, G.L.
History
DepositionDec 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 7, 2001Provider: 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 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE
E: TRIOSEPHOSPHATE ISOMERASE
F: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,02216
Polymers189,7908
Non-polymers1,2328
Water6,233346
1
A: TRIOSEPHOSPHATE ISOMERASE
B: TRIOSEPHOSPHATE ISOMERASE
C: TRIOSEPHOSPHATE ISOMERASE
D: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5118
Polymers94,8954
Non-polymers6164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: TRIOSEPHOSPHATE ISOMERASE
F: TRIOSEPHOSPHATE ISOMERASE
G: TRIOSEPHOSPHATE ISOMERASE
H: TRIOSEPHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5118
Polymers94,8954
Non-polymers6164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.000, 89.100, 145.100
Angle α, β, γ (deg.)90.00, 92.80, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.6803, -0.31876, 0.65999), (-0.31654, -0.68438, -0.65683), (0.66105, -0.65576, 0.36468)-23.834, 98.36513, 58.76599
2given(0.62704, -0.00728, -0.77895), (0.00306, -0.99993, 0.01181), (-0.77898, -0.00979, -0.62697)55.10153, 60.82224, 115.24031
3given(-0.93681, 0.32394, 0.13209), (0.32729, 0.67821, 0.65797), (0.12355, 0.65962, -0.74137)-6.37488, -36.65746, 96.46261
4given(0.99998, 0.00318, 0.00584), (-0.00319, 0.99999, 0.00161), (-0.00584, -0.00163, 0.99998)35.6823, 22.51346, 72.74033
5given(-0.67601, -0.32431, 0.66169), (-0.31563, -0.68397, -0.65769), (0.66587, -0.65346, 0.36001)12.35264, 121.03146, 131.69531
6given(0.62252, -0.01007, -0.78254), (0.0045, -0.99985, 0.01644), (-0.78259, -0.01376, -0.62239)91.66452, 83.0285, 187.68719
7given(-0.93656, 0.32639, 0.12778), (0.32599, 0.67712, 0.65973), (0.12881, 0.65953, -0.74056)30.10075, -14.10838, 169.0519

-
Components

#1: Protein
TRIOSEPHOSPHATE ISOMERASE


Mass: 23723.691 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: 2-CARBOXYETHYLPHOSPHONIC ACID IN THE ACTIVE SITE / Source: (gene. exp.) PYROCOCCUS WOESEI (archaea) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834
References: UniProt: P95583, UniProt: P62003*PLUS, triose-phosphate isomerase
#2: Chemical
ChemComp-3PP / 3-PHOSPHONOPROPANOIC ACID / 2-CARBOXYETHYLPHOSPHONIC ACID


Mass: 154.058 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7O5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCONVERTS D-GLYCERALDEHYDE 3-PHOSPHATE TO DIHYDROXY-ACETONE PHOSPHATE. PLAYS AN IMPORTANT ROLE IN ...CONVERTS D-GLYCERALDEHYDE 3-PHOSPHATE TO DIHYDROXY-ACETONE PHOSPHATE. PLAYS AN IMPORTANT ROLE IN SEVERAL METABOLIC PATHWAYS.
Sequence detailsTHE C-TERMINAL 15 RESIDUES LISTED IN THE SWISS-PROT ENTRY ARE INCORRECT. THE SWISS-PROT ENTRY WILL ...THE C-TERMINAL 15 RESIDUES LISTED IN THE SWISS-PROT ENTRY ARE INCORRECT. THE SWISS-PROT ENTRY WILL BE UPDATED SOON.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 55 %
Description: MAD DATA WERE USED TO DETERMINE THE STRUCTURE, CROSS- CRYSTAL AVERAGING AND PHASE EXTENSION USING IN-HOUSE DATA WERE USED IN REFINEMENT OF THE MODEL.
Crystal growpH: 4.6 / Details: 0.1M SODIUM ACETATE PH 4.0 AND 7% PEG 4000
Crystal grow
*PLUS
pH: 4 / Method: vapor diffusion, hanging drop / Details: Bell, G.S., (1998) Acta crystallog., D54, 1419.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mM2-carboxyethylphosphonic acid1reservoir
20.1 Msodium acetate1reservoir
37 %PEG40001reservoir
410 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9795,0.9796,0.9537
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97961
30.95371
ReflectionResolution: 3→30 Å / Num. obs: 25844 / % possible obs: 90.1 % / Observed criterion σ(I): 2.5 / Redundancy: 15 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 3→3.2 Å / Rmerge(I) obs: 0.112 / % possible all: 89.7
Reflection
*PLUS
Num. measured all: 386571
Reflection shell
*PLUS
% possible obs: 89.7 %

-
Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: NCS RESTRAINTS WERE USED THROUGHOUT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.286 5062 10 %RANDOM
Rwork0.254 ---
obs0.254 49927 98.1 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13232 0 72 346 13650
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.8 Å
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
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