[English] 日本語
Yorodumi
- PDB-7jh0: Crystallographic structure of glyceraldehyde-3-phosphate dehydrog... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jh0
TitleCrystallographic structure of glyceraldehyde-3-phosphate dehydrogenase from Schistosoma mansoni
Components(Glyceraldehyde-3-phosphate ...) x 2
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycolytic process / glucose metabolic process / NAD binding / NADP binding / cytosol
Similarity search - Function
Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesSchistosoma mansoni (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsBoreiko, S. / Silva, M. / Iulek, J.
CitationJournal: Biochimie / Year: 2021
Title: Structure determination and analyses of the GAPDH from the parasite Schistosoma mansoni, the first one from a platyhelminth.
Authors: Boreiko, S. / Silva, M. / Iulek, J.
History
DepositionJul 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
B: Glyceraldehyde-3-phosphate dehydrogenase
C: Glyceraldehyde-3-phosphate dehydrogenase
D: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,72511
Polymers145,9664
Non-polymers7597
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16880 Å2
ΔGint-77 kcal/mol
Surface area44390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.123, 80.123, 417.015
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

-
Components

-
Glyceraldehyde-3-phosphate ... , 2 types, 4 molecules ABCD

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / Major larval surface antigen / P-37


Mass: 36503.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli)
References: UniProt: P20287, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Protein Glyceraldehyde-3-phosphate dehydrogenase / GAPDH / Major larval surface antigen / P-37


Mass: 36455.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schistosoma mansoni (invertebrata) / Production host: Escherichia coli (E. coli)
References: UniProt: P20287, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)

-
Non-polymers , 5 types, 210 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.54 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.12 M Ethylene glycols (0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol) , 0.1 M Buffer system 1 pH 6.5 (0,1 M MES/Imidazole) and 30% ...Details: 0.12 M Ethylene glycols (0.3 M diethyleneglycol, 0.3 M triethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 M pentaethyleneglycol) , 0.1 M Buffer system 1 pH 6.5 (0,1 M MES/Imidazole) and 30% Mix of precipitants (20% V/V Glicerol e 10% w/V PEG 40,000)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.08
ReflectionResolution: 2.51→57.76 Å / Num. obs: 51375 / % possible obs: 99.9 % / Redundancy: 21.57 % / CC1/2: 0.999 / Rrim(I) all: 0.172 / Net I/σ(I): 14.35
Reflection shellResolution: 2.51→2.57 Å / Mean I/σ(I) obs: 1.13 / Num. unique obs: 3515 / CC1/2: 0.501 / Rrim(I) all: 2.654 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
XDS3.25data processing
PHENIXmodel building
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K9D

4k9d


Resolution: 2.51→57.76 Å / Cross valid method: THROUGHOUT / σ(F): 1.87 / Phase error: 35.86 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2726 1968 3.83 %
Rwork0.2132 49363 -
obs0.2158 51375 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.41 Å2 / Biso mean: 74.0242 Å2 / Biso min: 35.66 Å2
Refinement stepCycle: final / Resolution: 2.51→57.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9919 0 50 203 10172
Biso mean--82.25 57.37 -
Num. residues----1352
LS refinement shellResolution: 2.51→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.3314 139 -
Rwork0.3378 3523 -
all-3662 -
obs--96 %
Refinement TLS params.Method: refined / Origin x: -8.9134 Å / Origin y: 11.2973 Å / Origin z: -3.4192 Å
111213212223313233
T0.44 Å2-0.0994 Å2-0.0984 Å2-0.3196 Å2-0.0018 Å2--0.7127 Å2
L1.0325 °2-0.3296 °20.3037 °2-0.6516 °2-0.1299 °2--1.2204 °2
S-0.1876 Å °0.1113 Å °0.2704 Å °0.1141 Å °0.0208 Å °-0.018 Å °-0.0785 Å °-0.0509 Å °0.1083 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A or chain B or chain C or chain DA1 - 338
2X-RAY DIFFRACTION1chain A or chain B or chain C or chain DB1 - 338
3X-RAY DIFFRACTION1chain A or chain B or chain C or chain DC1 - 338
4X-RAY DIFFRACTION1chain A or chain B or chain C or chain DD1 - 338

+
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