[English] 日本語
Yorodumi
- PDB-2y6z: Crystallographic structure of GM23 an example of Catalytic migrat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y6z
TitleCrystallographic structure of GM23 an example of Catalytic migration from TIM to thiamin phosphate synthase.
ComponentsTRIOSE-PHOSPHATE ISOMERASETriosephosphate isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


glycosome / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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
PYROPHOSPHATE 2- / THIAMIN PHOSPHATE / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSaab-Rincon, G. / Olvera, L. / Olvera, M. / Rudino-Pinera, E. / Soberon, X. / Morett, E.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Evolutionary Walk between (Beta/Alpha)(8) Barrels: Catalytic Migration from Triosephosphate Isomerase to Thiamin Phosphate Synthase.
Authors: Saab-Rincon, G. / Olvera, L. / Olvera, M. / Rudino-Pinera, E. / Benites, E. / Soberon, X. / Morett, E.
History
DepositionJan 27, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 8, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIOSE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6793
Polymers27,1581
Non-polymers5212
Water1,53185
1
A: TRIOSE-PHOSPHATE ISOMERASE
hetero molecules

A: TRIOSE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3596
Polymers54,3162
Non-polymers1,0434
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area5370 Å2
ΔGint-19.9 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.300, 126.300, 107.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

-
Components

#1: Protein TRIOSE-PHOSPHATE ISOMERASE / Triosephosphate isomerase / GM23 / TIM


Mass: 27158.004 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIS PROTEIN IS RESULT OF ARTIFICIAL MUTATIONS IN ORDER TO OBTAIN A PROTEIN WITH THIAMIN PHOSPHATE SYNTHASE ACTIVITY STARTING FROM A TIM ACTIVITY.
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote)
Description: THE GENE FOR THE ENGINEERED GM23 WERE ORIGINALLY OBTAINED FROM TRYPANOSOMA BRUCEI
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): CM1061 THIE- / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-TPS / THIAMIN PHOSPHATE


Mass: 345.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N4O4PS
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 2 TO GLY ENGINEERED RESIDUE IN CHAIN A, SER 17 TO GLY ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, SER 2 TO GLY ENGINEERED RESIDUE IN CHAIN A, SER 17 TO GLY ENGINEERED RESIDUE IN CHAIN A, GLN 18 TO GLY ENGINEERED RESIDUE IN CHAIN A, SER 43 TO PRO ENGINEERED RESIDUE IN CHAIN A, THR 44 TO SER ENGINEERED RESIDUE IN CHAIN A, PHE 45 TO TRP ENGINEERED RESIDUE IN CHAIN A, VAL 46 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 47 TO MET ENGINEERED RESIDUE IN CHAIN A, LEU 48 TO GLN ENGINEERED RESIDUE IN CHAIN A, ILE 68 TO GLY ENGINEERED RESIDUE IN CHAIN A, ALA 69 TO ASN ENGINEERED RESIDUE IN CHAIN A, LYS 70 TO ALA ENGINEERED RESIDUE IN CHAIN A, SER 71 TO ASP ENGINEERED RESIDUE IN CHAIN A, SER 79 TO ALA ENGINEERED RESIDUE IN CHAIN A, PRO 81 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 82 TO SER ENGINEERED RESIDUE IN CHAIN A, VAL 88 TO ILE ENGINEERED RESIDUE IN CHAIN A, ASN 89 TO SER ENGINEERED RESIDUE IN CHAIN A, GLU 135 TO SER ENGINEERED RESIDUE IN CHAIN A, ALA 148 TO THR ENGINEERED RESIDUE IN CHAIN A, ILE 198 TO VAL
Sequence detailsTHE SEQUENCE DEPOSITED IN THIS ENTRY IS 88.1 PER CENT IDENTICAL TO UNIPROT P04789

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.3 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2 M LI2SO4, 100 MM MES, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 25, 2006
Details: DOUBLE CRYSTAL CHANNEL CUT, SI(111), 1M LONG RH COATED TOROIDAL MIRROR FOR VERTICAL AND HORIZONTAL FOCUSING
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→34 Å / Num. obs: 15823 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 50.84 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.6
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.8 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TRI

1tri


Resolution: 2.6→33.992 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.235 806 5.1 %
Rwork0.1935 --
obs0.1912 15799 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.848 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 57.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.8563 Å20 Å20 Å2
2--0.8563 Å20 Å2
3----1.7126 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.992 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1909 0 31 85 2025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121986
X-RAY DIFFRACTIONf_angle_d1.1962696
X-RAY DIFFRACTIONf_dihedral_angle_d19.128714
X-RAY DIFFRACTIONf_chiral_restr0.074302
X-RAY DIFFRACTIONf_plane_restr0.009343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6001-2.76290.37671360.32452454X-RAY DIFFRACTION99
2.7629-2.97620.3321450.28072444X-RAY DIFFRACTION99
2.9762-3.27540.27331320.21882486X-RAY DIFFRACTION99
3.2754-3.74890.2111270.16312511X-RAY DIFFRACTION100
3.7489-4.72120.18391450.12922499X-RAY DIFFRACTION98
4.7212-33.99530.25361210.17252599X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
1-0.2429-0.9643-0.8713-1.007-3.67784.67670.1228-0.23830.0890.54080.1530.4868-1.59090.2921-0.29740.62750.0562-0.01190.3888-0.20940.405557.3661-41.3358-19.1089
21.46720.0248-0.3746-1.1814-0.6430.7355-0.39710.2507-0.1766-1.12060.2209-0.6452-0.31560.15060.20020.7072-0.12750.18970.2140.0180.262363.9275-7.3238-12.6053
32.0643-1.3799-1.10170.2850.70422.79630.33260.45090.1939-1.6457-0.4457-0.5896-0.584-0.44780.00190.8732-0.03220.24830.22480.05740.285361.4945-11.1325-17.3349
40.30370.84110.79992.6718-1.09590.0184-0.1079-0.02550.2118-0.2160.06040.3516-0.08410.11020.01480.7426-0.04090.12250.32210.03530.383255.9829-1.9941-14.4611
51.9004-0.3817-0.49815.3313-1.31381.1161-0.1102-0.2297-0.01310.1416-0.02570.4453-0.5438-0.17570.10040.3897-0.03770.01220.1910.00490.21449.0201-10.321-0.0149
60.7140.2345-0.20121.3219-1.44520.5997-0.2178-0.1237-0.1742-0.29240.07820.07170.2803-0.10020.02970.3405-0.0496-0.00210.2142-0.01690.243648.4188-18.1547-0.0305
74.63021.13821.3629-0.45110.25911.4860.4328-0.004-0.62420.1173-0.2688-0.17450.61930.0157-0.11010.3983-0.02170.02450.23070.06210.364357.5246-26.20741.5673
82.6769-0.3471-0.46440.4535-1.32831.0321-0.2866-0.0466-0.8144-0.77190.0686-0.12020.34470.04730.140.4884-0.04270.04450.2191-0.02890.308955.0357-23.6425-5.768
90.99243.0982-1.05056.4171-2.05610.98960.0955-0.1694-0.3788-0.3585-0.1716-0.9311-0.055-0.29930.18890.54630.00140.08030.29430.04120.398661.4475-27.9435-7.0477
100.2979-0.03710.38871.26720.3935-0.37330.0406-0.05550.1316-0.0599-0.3259-0.77580.10130.25920.24490.5826-0.03330.17920.28450.10580.397666.9688-14.9778-11.0196
116.1501-4.58288.65587.5776-3.40028.5612-0.0597-0.4833-0.1871-0.46030.30740.6088-0.1557-3.6786-0.21110.43560.0742-0.05991.55070.1380.451859.4325-9.6-1.0105
126.8864-0.9672-7.06546.44464.37351.1197-0.4031-0.2831-0.19110.19990.11140.41560.03810.08780.18130.3263-0.34780.13540.81520.21681.200155.6943-1.88412.5779
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 9:22)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 23:47)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 48:65)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 66:94)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 95:155)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 156:190)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 191:208)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 209:235)
9X-RAY DIFFRACTION9CHAIN A AND (RESSEQ 236:244)
10X-RAY DIFFRACTION10CHAIN A AND (RESSEQ 245:265)
11X-RAY DIFFRACTION11CHAIN A AND (RESSEQ 1266)
12X-RAY DIFFRACTION12CHAIN A AND (RESSEQ 1267)

+
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