[English] 日本語
Yorodumi
- PDB-5cg7: Leishmania siamensis Triosephosphate isomerase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5cg7
TitleLeishmania siamensis Triosephosphate isomerase
ComponentsTriosephosphate isomerase
KeywordsHYDROLASE / TIM barrel / C2 structure / cacodylate binding Cys57
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process / 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
Triosephosphate isomerase
Similarity search - Component
Biological speciesLeishmania sp. 'siamensis' (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
Model detailsC2 structure, cacodylate modified Cys57
AuthorsKuaprasert, B. / Riangrungroj, P. / Pornthanakasem, W. / Attarataya, J. / Sirimontree, P. / Mungthin, M. / Leelayoova, S. / Suginta, W. / Choowongkomon, K. / Leartsakulpanich, U.
Funding support Thailand, 2items
OrganizationGrant numberCountry
Synchrotron Light Research Institute (Public Organization)SLRI; GRANT 2-2549/LS01 Thailand
National Center for Genetic Engineering and Biotechnology (BIOTEC)P-00-0029 Thailand
CitationJournal: To Be Published
Title: Crystal structure of Leishmania siamensis Triosephosphate isomerase at 1.88 Angstroms
Authors: Kuaprasert, B. / Riangrungroj, P. / Pornthanakasem, W. / Sirimontree, P. / Attarataya, J. / Mungthin, M. / Leelayoova, S. / Suginta, W. / Choowongkomon, K. / Leartsakulpanich, U.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8814
Polymers58,6972
Non-polymers1842
Water8,539474
1
A: Triosephosphate isomerase
hetero molecules

A: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8814
Polymers58,6972
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3260 Å2
ΔGint-23 kcal/mol
Surface area19400 Å2
MethodPISA
2
B: Triosephosphate isomerase
hetero molecules

B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8814
Polymers58,6972
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3240 Å2
ΔGint-23 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.440, 76.450, 94.940
Angle α, β, γ (deg.)90.000, 101.140, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Triosephosphate isomerase /


Mass: 29348.463 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania sp. 'siamensis' (eukaryote) / Gene: tim / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: I2APN2, triose-phosphate isomerase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.71 Å3/Da / Density % sol: 54.63 % / Description: rod shape
Crystal growTemperature: 298 K / Method: microbatch / pH: 5.9
Details: 0.2M calcium acetate hydrate, 0.1M sodium cacodylate trihydrate, 18% PEG 8000
PH range: 5.9

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: under LN2 cryostream
Diffraction sourceSource: SYNCHROTRON / Site: SLRI / Beamline: BL7.2W / Wavelength: 1.55 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 11, 2015 / Details: diffractometer mounted on MarDTB
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.55 Å / Relative weight: 1
ReflectionRedundancy: 2.8 % / Number: 130363 / Rsym value: 0.077 / D res high: 1.879 Å / D res low: 93.151 Å / Num. obs: 46171 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsRsym valueRedundancy
5.9321.5610.0310.0312.9
4.195.9310.0330.0332.9
3.424.1910.0370.0372.9
2.973.4210.0470.0472.9
2.652.9710.0730.0732.9
2.422.6510.0970.0972.8
2.242.4210.1320.1322.8
2.12.2410.1760.1762.8
1.982.110.2610.2612.8
1.881.9810.4580.4582.7
ReflectionResolution: 1.879→93.151 Å / Num. all: 46171 / Num. obs: 46171 / % possible obs: 98.6 % / Redundancy: 2.8 % / Rpim(I) all: 0.055 / Rrim(I) all: 0.095 / Rsym value: 0.077 / Net I/av σ(I): 8.245 / Net I/σ(I): 9.8 / Num. measured all: 130363
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
1.88-1.982.70.4581.41676962330.3330.4582.391.4
1.98-2.12.80.2612.11782064360.1890.2614100
2.1-2.242.80.17641701560750.1270.1765.7100
2.24-2.422.80.13251585056250.0960.1327.4100
2.42-2.652.80.0977.51487852290.0690.0979.4100
2.65-2.972.90.0739.81349447090.0520.07311.9100
2.97-3.422.90.04714.31193341350.0330.04716.8100
3.42-4.192.90.03717.21029735310.0260.03721.399.9
4.19-5.932.90.03317.8799127260.0230.03320.999.5
5.93-21.5632.90.03119.6431614720.0210.03120.496.3

-
Processing

Software
NameVersionClassification
AUTOMAR2.1data collection
MOSFLM7.1.1data reduction
SCALA3.3.22data scaling
MOLREP09.12.2013phasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GNJ

4gnj


Resolution: 1.88→93.15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.1821 / WRfactor Rwork: 0.1561 / FOM work R set: 0.8459 / SU B: 3.082 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1285 / SU Rfree: 0.1171 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1962 2315 5 %RANDOM
Rwork0.1684 ---
obs0.1698 43856 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.52 Å2 / Biso mean: 18.869 Å2 / Biso min: 6.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20.54 Å2
2---0.8 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 1.88→93.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 24 474 4239
Biso mean--12.25 25.52 -
Num. residues----491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0193848
X-RAY DIFFRACTIONr_angle_refined_deg1.9651.9535232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4525493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.75225.263152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98115641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9521514
X-RAY DIFFRACTIONr_chiral_restr0.1410.2615
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212836
X-RAY DIFFRACTIONr_mcbond_it1.5611.6741966
X-RAY DIFFRACTIONr_mcangle_it2.2612.4892452
X-RAY DIFFRACTIONr_scbond_it2.7631.8881882
LS refinement shellResolution: 1.879→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 164 -
Rwork0.322 2939 -
all-3103 -
obs--90.81 %

+
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