[English] 日本語
Yorodumi
- PDB-8jzj: E.coli Glyceraldehyde-3-phosphate dehydrogenase structure under c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8jzj
TitleE.coli Glyceraldehyde-3-phosphate dehydrogenase structure under cryoprotect condition of ammonium sulfate
ComponentsGlyceraldehyde-3-phosphate dehydrogenase
KeywordsOXIDOREDUCTASE / Glycolysis / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glucose metabolic process / NAD binding / NADP binding
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / 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
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsJang, K. / Hlaing, S.H.S. / Kim, H.G. / Kim, N. / Choe, H.W. / Kim, Y.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2021R1I1A3060013 Korea, Republic Of
CitationJournal: Cryst.Growth Des. / Year: 2023
Title: Strategy to Select an Appropriate Cryoprotectant for an X-ray Study of Escherichia coli GAPDH Crystals
Authors: Hlaing, S.H.S. / Jang, K. / Kim, H.G. / Kim, N. / Lee, K.J. / Choe, H.W. / Park, J.H. / Kim, Y.J.
History
DepositionJul 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glyceraldehyde-3-phosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5422
Polymers35,4461
Non-polymers961
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.971, 121.971, 155.134
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-513-

HOH

21A-728-

HOH

31A-759-

HOH

41A-764-

HOH

-
Components

#1: Protein Glyceraldehyde-3-phosphate dehydrogenase


Mass: 35446.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: gapA / Production host: Escherichia coli (E. coli) / References: UniProt: C3T6W2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 4.05 Å3/Da / Density % sol: 69.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2.7 M ammonium sulfate, 0.1 M MES / PH range: 5.6 - 6.4

-
Data collection

DiffractionMean temperature: 277 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.99→47.94 Å / Num. obs: 39834 / % possible obs: 99.3 % / Redundancy: 11 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.016 / Rrim(I) all: 0.053 / Χ2: 0.99 / Net I/av σ(I): 30.1 / Net I/σ(I): 30.1
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 11 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 8.4 / Num. unique obs: 2880 / Rpim(I) all: 0.085 / Rrim(I) all: 0.283 / % possible all: 98.5

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→39.33 Å / SU ML: 0.18 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 2023 5.08 %0.2033
Rwork0.1755 ---
obs0.1769 39810 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→39.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2484 0 5 266 2755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082530
X-RAY DIFFRACTIONf_angle_d0.9753427
X-RAY DIFFRACTIONf_dihedral_angle_d6.296349
X-RAY DIFFRACTIONf_chiral_restr0.062401
X-RAY DIFFRACTIONf_plane_restr0.01441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.040.2471450.20922627X-RAY DIFFRACTION98
2.04-2.10.21251360.18342702X-RAY DIFFRACTION100
2.1-2.160.20491360.17042671X-RAY DIFFRACTION100
2.16-2.230.1921270.16482703X-RAY DIFFRACTION100
2.23-2.310.19211500.17032674X-RAY DIFFRACTION100
2.31-2.40.23491390.17512692X-RAY DIFFRACTION100
2.4-2.510.19021500.18952676X-RAY DIFFRACTION100
2.51-2.640.21111530.18212701X-RAY DIFFRACTION100
2.65-2.810.20911320.18282719X-RAY DIFFRACTION100
2.81-3.030.22891500.20212701X-RAY DIFFRACTION100
3.03-3.330.18771530.18582722X-RAY DIFFRACTION100
3.33-3.810.2141470.15952734X-RAY DIFFRACTION100
3.81-4.80.17091490.14262759X-RAY DIFFRACTION100
4.8-39.330.22121560.1972706X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: 41.922 Å / Origin y: -1.8586 Å / Origin z: 24.2317 Å
111213212223313233
T0.2254 Å20.0117 Å2-0.0688 Å2-0.2043 Å2-0.0076 Å2--0.251 Å2
L0.6592 °20.5209 °2-0.0908 °2-0.681 °2-0.0546 °2--0.3558 °2
S-0.1032 Å °0.111 Å °0.1925 Å °-0.1511 Å °0.0401 Å °0.2852 Å °-0.0242 Å °-0.0678 Å °-0.0136 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