[English] 日本語
Yorodumi
- PDB-1lyx: Plasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphogl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1lyx
TitlePlasmodium Falciparum Triosephosphate Isomerase (PfTIM)-Phosphoglycolate complex
ComponentsTriosephosphate Isomerase
KeywordsISOMERASE / TIM barrels / beta-alpha barrels
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / glycolytic process / gluconeogenesis / identical protein binding / 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 speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsParthasarathy, S. / Balaram, H. / Balaram, P. / Murthy, M.R.
Citation
Journal: Biochemistry / Year: 2002
Title: Structure of the Plasmodium falciparum triosephosphate isomerase-phosphoglycolate complex in two crystal forms: characterization of catalytic loop open and closed conformations in the ligand-bound state
Authors: Parthasarathy, S. / Ravindra, G. / Balaram, H. / Balaram, P. / Murthy, M.R.
#1: Journal: Structure / Year: 1997
Title: Triosephosphate isomerase from Plasmodium falciparum: Crystal structure provides insights into antimalarial drug design
Authors: Velankar, S.S. / Ray, S.S. / Gokhle, R.S. / Suma, S. / Balaram, H. / Balaram, P. / Murthy, M.R.N.
History
DepositionJun 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triosephosphate Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1542
Polymers27,9981
Non-polymers1561
Water3,117173
1
A: Triosephosphate Isomerase
hetero molecules

A: Triosephosphate Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3084
Polymers55,9952
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
2
A: Triosephosphate Isomerase
hetero molecules

A: Triosephosphate Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3084
Polymers55,9952
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4080 Å2
ΔGint-34 kcal/mol
Surface area19720 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)88.242, 63.437, 53.886
Angle α, β, γ (deg.)90.00, 117.74, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

-
Components

#1: Protein Triosephosphate Isomerase / E.C.5.3.1.1 / TIM / triose-phosphate isomerase / triose phosphate isomerase


Mass: 27997.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: TPI / Plasmid: ptrc 99A vector, called pARC / Production host: Escherichia coli (E. coli) / Strain (production host): AA200 / References: UniProt: Q07412, 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.: 173 / 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: 2.4 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 12% to 25% PEG 6000 or PEG 4000 or PEG 3350 or PEG 1450 in the presence of EDTA, DTT and Sodium azide in 100mM MES. pH 6.5, VAPOR DIFFUSION, HANGING DROP at 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112-25 %PEG60001reservoir
2100 mMMES1reservoirpH6.5
30.05 mMdithiothreitol1reservoir
40.05 mMEDTA1reservoir
50.05 mM1reservoirNaN3
615 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 10, 2000 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 20508 / Num. obs: 20508 / % possible obs: 98.4 % / Redundancy: 18.8 % / Rsym value: 0.068
Reflection shellResolution: 1.9→1.97 Å / Num. unique all: 2008 / Rsym value: 0.215 / % possible all: 97.1
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. obs: 10508 / Num. measured all: 198026 / Rmerge(I) obs: 0.068

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Monomer of unbound PfTIM, PDB code 1YDV

1ydv


Resolution: 1.9→20 Å / Data cutoff high absF: 416213.98 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.1 / Stereochemistry target values: Engh & Huber
Details: Bulk solvent and anisotropic B-scaling were applied throughout the refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1977 9.9 %Random
Rwork0.18 ---
all-20508 --
obs-20037 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.54 Å2 / ksol: 0.355873 e/Å3
Displacement parametersBiso mean: 23.74 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å2-4.32 Å22.14 Å2
2--0 Å24.14 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1957 0 9 173 2139
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0062
X-RAY DIFFRACTIONc_angle_deg1.3524
X-RAY DIFFRACTIONc_dihedral_angle_d22.3443
X-RAY DIFFRACTIONc_improper_angle_d0.7165
X-RAY DIFFRACTIONc_mcbond_it3.191.5
X-RAY DIFFRACTIONc_mcangle_it3.82
X-RAY DIFFRACTIONc_scbond_it5.82
X-RAY DIFFRACTIONc_scangle_it8.142.5
LS refinement shellResolution: 1.9→1.97 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.271 172 8.31 %
Rwork0.233 1714 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3pg.parpg.top
Refinement
*PLUS
Highest resolution: 1.9 Å / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.352
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3443
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.7165

+
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