[English] 日本語
Yorodumi
- PDB-3th6: Crystal structure of Triosephosphate isomerase from Rhipicephalus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3th6
TitleCrystal structure of Triosephosphate isomerase from Rhipicephalus (Boophilus) microplus.
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / ALPHA/BETA BARREL / EMBRYOGENESIS / GLYCOLYSIS
Function / homology
Function and homology information


triose-phosphate isomerase / triose-phosphate isomerase activity / gluconeogenesis / glycolytic process
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 speciesRhipicephalus microplus (southern cattle tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsArreola, R. / Rodriguez-Romero, A. / Moraes, J. / Gomez-Puyou, A. / Perez-Montfort, R. / Logullo, C.
CitationJournal: Insect Biochem.Mol.Biol. / Year: 2011
Title: Structural and biochemical characterization of a recombinant triosephosphate isomerase from Rhipicephalus (Boophilus) microplus.
Authors: Moraes, J. / Arreola, R. / Cabrera, N. / Saramago, L. / Freitas, D. / Masuda, A. / da Silva Vaz, I. / Tuena de Gomez-Puyou, M. / Perez-Montfort, R. / Gomez-Puyou, A. / Logullo, C.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Triosephosphate isomerase
B: Triosephosphate isomerase


Theoretical massNumber of molelcules
Total (without water)54,2282
Polymers54,2282
Non-polymers00
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.384, 53.384, 278.775
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Triosephosphate isomerase /


Mass: 27114.059 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Total RNA was isolated from 10-day-old eggs
Source: (gene. exp.) Rhipicephalus microplus (southern cattle tick)
Strain: Porto Alegre / Gene: TIM / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYS / References: UniProt: A8B3A8, triose-phosphate isomerase
#2: Water ChemComp-HOH / water / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES/Na, 1.4 M Trisodium citrate dihydrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.977 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 2.4→46.474 Å / Num. all: 17583 / Num. obs: 17583 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.5 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.102 / Rsym value: 0.102 / Net I/σ(I): 17.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value
2.4-2.538.70.37522232925620.375
2.53-2.688.70.2742.22097624240.274
2.68-2.878.70.1941953222570.19
2.87-3.18.50.1395.21798621270.139
3.1-3.398.40.0977.11640419480.097
3.39-3.798.30.0777.91465117730.077
3.79-4.388.30.0715.81294115600.071
4.38-5.378.50.0796.81128613260.079
5.37-7.598.80.0648.9905110230.064

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.46 Å
Translation2.5 Å46.46 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
PHASER1.3.2phasing
CNS1.2refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WYI

1wyi


Resolution: 2.4→46.46 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 1907544 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: BULK SOLVENT MODEL USED THE FOLLOWING RESIDUES ARE DISORDERED AND IT WERE NOT MODELED DUE TO POOR/NULL ELECTRON DENSITY. CHAIN A/B RESIDUES: MET1 AND ALA2. CHAIN A RESIDUES FROM LOOP6: ...Details: BULK SOLVENT MODEL USED THE FOLLOWING RESIDUES ARE DISORDERED AND IT WERE NOT MODELED DUE TO POOR/NULL ELECTRON DENSITY. CHAIN A/B RESIDUES: MET1 AND ALA2. CHAIN A RESIDUES FROM LOOP6: THR172, GLY173 AND LYS174. CHAIN B RESIDUES FROM LOOP6: GLY171 THR172, GLY173, LYS174 AND THR175. CHAIN B RESIDUE: GLY249
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1773 10.1 %RANDOM
Rwork0.186 ---
obs0.221 17481 99.9 %-
all-17583 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.5156 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 80.29 Å2 / Biso mean: 29.8919 Å2 / Biso min: 8.29 Å2
Baniso -1Baniso -2Baniso -3
1-3.82 Å20 Å20 Å2
2--3.82 Å20 Å2
3----7.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3716 0 0 112 3828
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.232
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.303 285 9.7 %
Rwork0.238 2640 -
all-2925 -
obs-2640 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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