[English] 日本語
Yorodumi
- PDB-1amk: LEISHMANIA MEXICANA TRIOSE PHOSPHATE ISOMERASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1amk
TitleLEISHMANIA MEXICANA TRIOSE PHOSPHATE ISOMERASE
ComponentsTRIOSE PHOSPHATE ISOMERASE
KeywordsGLUCONEOGENESIS / TIM / 2-PG / PGA / FATTY ACID BIOSYNTHESIS
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 / 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
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsWilliams, J.C. / Wierenga, R.
Citation
Journal: Protein Eng. / Year: 1999
Title: Structural and mutagenesis studies of leishmania triosephosphate isomerase: a point mutation can convert a mesophilic enzyme into a superstable enzyme without losing catalytic power.
Authors: Williams, J.C. / Zeelen, J.P. / Neubauer, G. / Vriend, G. / Backmann, J. / Michels, P.A. / Lambeir, A.M. / Wierenga, R.K.
#1: Journal: Eur.J.Biochem. / Year: 1994
Title: Triose-Phosphate Isomerase of Leishmania Mexicana Mexicana. Cloning and Characterization of the Gene, Overexpression in Escherichia Coli and Analysis of the Protein
Authors: Kohl, L. / Callens, M. / Wierenga, R.K. / Opperdoes, F.R. / Michels, P.A.
History
DepositionJun 17, 1997Processing site: BNL
Revision 1.0Dec 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRIOSE PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3652
Polymers27,2091
Non-polymers1561
Water2,018112
1
A: TRIOSE PHOSPHATE ISOMERASE
hetero molecules

A: TRIOSE PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7314
Polymers54,4182
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3720 Å2
ΔGint-32 kcal/mol
Surface area19010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)99.090, 52.940, 58.850
Angle α, β, γ (deg.)90.00, 118.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

-
Components

#1: Protein TRIOSE PHOSPHATE ISOMERASE


Mass: 27209.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania mexicana (eukaryote) / References: UniProt: P48499, triose-phosphate isomerase
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 5.85
Details: 100 MM ACETIC ACID/NAOH 4.5 20% PEG 6000 1 MM DTT, EDTA, 1 MM AZIDE, 5% ETHYLENE GLYCOL, 10 MM 2-PHOSPHOGLYCOLIC ACID. CRYSTAL WAS MOVED INTO 100 MM CITRATE PH 5.85 20 % PEG 6000, 1 MM DTT, ...Details: 100 MM ACETIC ACID/NAOH 4.5 20% PEG 6000 1 MM DTT, EDTA, 1 MM AZIDE, 5% ETHYLENE GLYCOL, 10 MM 2-PHOSPHOGLYCOLIC ACID. CRYSTAL WAS MOVED INTO 100 MM CITRATE PH 5.85 20 % PEG 6000, 1 MM DTT, 1 MM EDTA, 1 MM AZIDE BEFORE DATA COLLECTION.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
111 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
325 mM1dropNaCl
41 mMEDTA1drop
51 mMdithiothreitol1drop
61 mM1dropNaN3
720 %PEG60001reservoir
81 mMEDTA1reservoir
91 mMdithiothreitol1reservoir
101 mM1reservoirNaN3
11100 mMacetic acid-NaOH1reservoirpH4.5

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceWavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Feb 22, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→22 Å / Num. obs: 22669 / % possible obs: 89.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 20.8
Reflection shellResolution: 1.8→1.83 Å / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 6 / % possible all: 84.3
Reflection
*PLUS
Lowest resolution: 22 Å / Num. measured all: 123706 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 84.3 % / Rmerge(I) obs: 0.116

-
Processing

Software
NameVersionClassification
AMoREphasing
TNT5Drefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5TIM

5tim


Resolution: 1.83→22 Å / Isotropic thermal model: TNT BCORREL V1.0 / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
Rwork0.107 --
obs-21346 88 %
Solvent computationSolvent model: BABINET / Bsol: 262.9 Å2 / ksol: 0.802 e/Å3
Refinement stepCycle: LAST / Resolution: 1.83→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 9 112 2027
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01619506
X-RAY DIFFRACTIONt_angle_deg2.80826443
X-RAY DIFFRACTIONt_dihedral_angle_d17.55211593
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.017488
X-RAY DIFFRACTIONt_gen_planes0.01628025
X-RAY DIFFRACTIONt_it6.07519500.21
X-RAY DIFFRACTIONt_nbd0.01566240
Refinement
*PLUS
Rfactor all: 0.107 / Rfactor Rwork: 0.107
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_planar_d0.0178
X-RAY DIFFRACTIONt_plane_restr0.01625

+
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