[English] 日本語
Yorodumi
- PDB-2j27: The functional role of the conserved active site proline of trios... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j27
TitleThe functional role of the conserved active site proline of triosephosphate isomerase.
ComponentsTRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
KeywordsISOMERASE / TIM / 2PG / LOOP7 / GLYCOSOME / TIM-BARREL / GLUCONEOGENESIS / LIPID SYNTHESIS / ATOMIC RESOLUTION / GLYCOLYSIS / PENTOSE SHUNT / POINT MUTATION / FATTY ACID BIOSYNTHESIS / 2-PHOSPHO GLYCOLATE / PROTEIN ENGINEERING
Function / homology
Function and homology information


glycosome / 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, 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
2-PHOSPHOGLYCOLIC ACID / Triosephosphate isomerase, glycosomal
Similarity search - Component
Biological speciesTRYPANOSOMA BRUCEI BRUCEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsCasteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K.
CitationJournal: Biochemistry / Year: 2006
Title: Functional Role of the Conserved Active Site Proline of Triosephosphate Isomerase.
Authors: Casteleijn, M.G. / Alahuhta, M. / Groebel, K. / El-Sayed, I. / Augustyns, K. / Lambeir, A.M. / Neubauer, P. / Wierenga, R.K.
History
DepositionAug 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: 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 1.4Dec 13, 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
Revision 1.5May 1, 2024Group: Structure summary / Category: struct / Item: _struct.title
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" AND "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-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 GLYCOSOMAL
B: TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0885
Polymers53,6802
Non-polymers4083
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.810, 97.320, 112.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.724, -0.69), (0.024, -0.999, -0.025), (-0.689, -0.034, 0.724)
Vector: 1.31264, -0.03957, 0.21347)

-
Components

#1: Protein TRIOSEPHOSPHATE ISOMERASE GLYCOSOMAL / TIM / TRIOSE-PHOSPHATE ISOMERASE


Mass: 26839.795 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA BRUCEI BRUCEI (eukaryote) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04789, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PRO 168 TO ALA ENGINEERED RESIDUE IN CHAIN B, PRO 168 TO ALA

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growpH: 9.5
Details: WELL SOLUTION: 0.1 M CHES PH 9.5, 25 % PEG 1500, 200 MM MGSO4 PROTEIN SOLUTION: 11.5 MG/ML PROTEIN, 20 MM TRIS/HCL PH 7, 100 MM NACL, 1 MM DTT, 1 MM EDTA, 1 MM NAN3 AND 10 MM 2PG

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9023
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2005 / Details: RH COATED, ZERODUR
RadiationMonochromator: FIXED EXIT DOUBLE CRYSTAL SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9023 Å / Relative weight: 1
ReflectionResolution: 1.15→25 Å / Num. obs: 164758 / % possible obs: 92 % / Observed criterion σ(I): 3 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.12
Reflection shellResolution: 1.15→1.2 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 5.29 / % possible all: 76.3

-
Processing

Software
NameClassification
SHELXL-97refinement
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIM

5tim


Resolution: 1.15→25 Å / Num. parameters: 40486 / Num. restraintsaints: 48408 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 8251 5 %RANDOM
obs0.1417 -91.8 %-
all-164768 --
Refine analyzeNum. disordered residues: 10 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 17876
Refinement stepCycle: LAST / Resolution: 1.15→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3760 0 23 686 4469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.0309
X-RAY DIFFRACTIONs_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.076
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.043
X-RAY DIFFRACTIONs_approx_iso_adps0.081

+
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