[English] 日本語
Yorodumi
- PDB-7pej: Crystal structure of Triosephosphate Isomerase from Schizosacchar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pej
TitleCrystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM wt)
ComponentsTriosephosphate isomerase
KeywordsISOMERASE / TIM / TIM barrel / Glycolytic enzyme
Function / homology
Function and homology information


Glycolysis / Gluconeogenesis / triose-phosphate isomerase / triose-phosphate isomerase activity / canonical glycolysis / glyceraldehyde-3-phosphate biosynthetic process / glycerol catabolic process / gluconeogenesis / glycolytic process / 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-type TIM barrel
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Triosephosphate isomerase
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRomero-Romero, S. / Garza-Ramos, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: To Be Published
Title: Crystal structure of Triosephosphate Isomerase from Schizosaccharomyces pombe (SpTIM wt)
Authors: Romero-Romero, S. / Garza-Ramos, G.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V.
History
DepositionAug 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,33114
Polymers108,5194
Non-polymers81110
Water15,403855
1
A: Triosephosphate isomerase
B: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6667
Polymers54,2602
Non-polymers4065
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-74 kcal/mol
Surface area18060 Å2
MethodPISA
2
C: Triosephosphate isomerase
D: Triosephosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6657
Polymers54,2602
Non-polymers4055
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-62 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.510, 149.510, 99.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein
Triosephosphate isomerase / TIM / Triose-phosphate isomerase


Mass: 27129.814 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: tpi1, tpi, SPCC24B10.21 / Plasmid: pET24a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07669, triose-phosphate isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 2.2 M Ammonium sulphate, 0.2 M Lithium acetate, 9.1 mg/mL protein concentration

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 20, 2021
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.79→37.38 Å / Num. obs: 103063 / % possible obs: 99.77 % / Redundancy: 7.6 % / Biso Wilson estimate: 36.36 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.09633 / Rpim(I) all: 0.03754 / Rrim(I) all: 0.1035 / Net I/σ(I): 13.11
Reflection shellResolution: 1.79→1.854 Å / Redundancy: 7.6 % / Rmerge(I) obs: 1.437 / Mean I/σ(I) obs: 0.99 / Num. unique obs: 10149 / CC1/2: 0.307 / CC star: 0.64 / Rpim(I) all: 0.9385 / Rrim(I) all: 0.915 / % possible all: 98.26

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FF7

4ff7


Resolution: 1.79→37.38 Å / SU ML: 0.3221 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.1053
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2179 2100 2.04 %
Rwork0.1817 100929 -
obs0.1825 103029 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.25 Å2
Refinement stepCycle: LAST / Resolution: 1.79→37.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7366 0 46 855 8267
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01517522
X-RAY DIFFRACTIONf_angle_d1.306510196
X-RAY DIFFRACTIONf_chiral_restr0.08351177
X-RAY DIFFRACTIONf_plane_restr0.01051325
X-RAY DIFFRACTIONf_dihedral_angle_d7.10381027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.830.61521370.53726567X-RAY DIFFRACTION97.39
1.83-1.880.49711390.41626673X-RAY DIFFRACTION100
1.88-1.930.31621390.30456707X-RAY DIFFRACTION99.94
1.93-1.990.32391400.26096725X-RAY DIFFRACTION99.97
1.99-2.050.27971410.24076753X-RAY DIFFRACTION100
2.05-2.120.27241390.23156704X-RAY DIFFRACTION100
2.12-2.210.27831400.22696731X-RAY DIFFRACTION100
2.21-2.310.23411400.1926706X-RAY DIFFRACTION99.99
2.31-2.430.22791400.18976726X-RAY DIFFRACTION100
2.43-2.580.2371400.1966749X-RAY DIFFRACTION100
2.58-2.780.24781410.1866755X-RAY DIFFRACTION100
2.78-3.060.21071400.17886748X-RAY DIFFRACTION100
3.06-3.50.2251400.16546757X-RAY DIFFRACTION100
3.5-4.410.15761410.13746768X-RAY DIFFRACTION100
4.41-37.380.17531430.1546860X-RAY DIFFRACTION99.52
Refinement TLS params.Method: refined / Origin x: 15.1488993668 Å / Origin y: 32.0074573593 Å / Origin z: -34.1968980036 Å
111213212223313233
T0.256833112697 Å2-0.0267271674031 Å2-0.0292696612469 Å2-0.216928710417 Å20.0638315485604 Å2--0.300135966137 Å2
L0.399278810752 °20.0834259767506 °2-0.354716423525 °2-0.265429798803 °20.0529045158442 °2--1.31482326443 °2
S0.00334399992638 Å °0.015328554019 Å °0.104954355147 Å °-0.0418311627534 Å °-0.00358169788535 Å °-0.031866015838 Å °0.0678284744428 Å °-0.0352106806812 Å °0.00458357344633 Å °
Refinement TLS groupSelection details: all

+
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