[English] 日本語
Yorodumi
- PDB-2gd1: COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gd1
TitleCOENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS
ComponentsAPO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE(ALDEHYDE(D)-NAD(A))
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 / cytoplasm
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 / Dihydrodipicolinate Reductase; domain 2 ...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 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsSkarzynski, T. / Wonacott, A.J.
Citation
Journal: J.Mol.Biol. / Year: 1988
Title: Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.
Authors: Skarzynski, T. / Wonacott, A.J.
#1: Journal: Gene / Year: 1989
Title: Nucleotide Sequence Determination of the DNA Region Coding for Bacillus Stearothermophilus Glyceraldehyde-3-Phosphate Dehydrogenase and of the Flanking DNA Regions Required for its Expression in Escherichia Coli
Authors: Branlant, C. / Oster, T. / Branlant, G.
#2: Journal: J.Mol.Biol. / Year: 1987
Title: Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 Angstroms Resolution
Authors: Skarzynski, T. / Moody, P.C.E. / Wonacott, A.J.
#3: Journal: J.Mol.Biol. / Year: 1984
Title: Structural Evidence for Ligand-Induced Sequential Conformational Changes in Glyceraldehyde 3-Phosphate Dehydrogenase
Authors: Leslie, A.G.W. / Wonacott, A.J.
#4: Journal: J.Mol.Biol. / Year: 1983
Title: Coenzyme Binding in Crystals of Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Leslie, A.G.W. / Wonacott, A.J.
#5: Journal: Philos.Trans.R.Soc.London,Ser.B / Year: 1981
Title: Glyceraldehyde-3-Phosphate Dehydrogenase
Authors: Dalziel, K. / Mcferran, N.V. / Wonacott, A.J.
#6: Journal: Proc.FEBS Meet. / Year: 1978
Title: Enzymes from Thermophilic Bacteria
Authors: Walker, J.E.
#7: Journal: Nature / Year: 1977
Title: Sequence and Structure of D-Glyceraldehyde 3-Phosphate Dehydrogenase from Bacillus Stearothermophilus
Authors: Biesecker, G. / Harris, J.I. / Thierry, J.C. / Walker, J.E. / Wonacott, A.J.
#8: Journal: Biochem.Soc.Trans. / Year: 1977
Title: Coenzyme Binding and Co-Operativity in D-Glyceraldehyde 3-Phosphate Dehydrogenase
Authors: Biesecker, G. / Wonacott, A.J.
#9: Journal: FEBS Lett. / Year: 1971
Title: Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus
Authors: Suzuki, K. / Harris, J.I.
History
DepositionJun 29, 1989Processing site: BNL
Revision 1.0Oct 15, 1989Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
O: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
P: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
Q: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
R: APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,73312
Polymers143,9644
Non-polymers7698
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17110 Å2
ΔGint-216 kcal/mol
Surface area44530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.800, 129.200, 83.100
Angle α, β, γ (deg.)90.00, 107.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.33306, -0.05375, 0.94137), (-0.05375, -0.99567, -0.07587), (0.94137, -0.07587, 0.32871)-13.05, 29.27, 10.92
2given(-0.99999, -0.00386, 0.00023), (-0.00385, 0.99317, 0.11654), (-0.00023, 0.11654, -0.99318)-11.38, -0.69, 11.46
3given(0.33305, 0.05761, -0.94114), (0.05761, -0.99751, -0.04067), (-0.94114, -0.04067, -0.33555)1.56, 29.7, 4.02
DetailsTHE TRANSFORMATION PROVIDED ON THE *MTRIX 1* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *P* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 2* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *Q* WHEN APPLIED TO CHAIN *O*. THE TRANSFORMATION PROVIDED ON THE *MTRIX 3* RECORDS BELOW YIELDS APPROXIMATE COORDINATES FOR CHAIN *R* WHEN APPLIED TO CHAIN *O*.

-
Components

#1: Protein
APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE


Mass: 35991.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Cell line: 293
References: UniProt: P00362, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM ...THE NUMBERING SCHEME USED IN THIS ENTRY MAXIMIZES THE HOMOLOGY BETWEEN SEQUENCES OF GAPDH FROM VARIOUS SOURCES. THE AMINO ACID SEQUENCE USED IS BASED ON THE GENE SEQUENCE (SEE REFERENCE 1 ABOVE) AND CONTAINS 20 DIFFERENCES FROM THE SEQUENCE GIVEN IN REFERENCE 7 ABOVE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal grow
*PLUS
pH: 6.6 / Method: microdialysis / Details: referred to FEBS Lett.13.217-220
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.33 Mammonium sulfate12
210 mMTris-HCl12
32 mMEDTA12
55 mg/mlprotein11
62.5 Mammonium sulfate11
4DTT12

-
Data collection

Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 55743 / % possible obs: 95.4 % / Rmerge(I) obs: 0.098 / Num. measured all: 183964

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 2.5 Å /
RfactorNum. reflection
obs0.177 53315
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10100 0 40 504 10644
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0410.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.881
X-RAY DIFFRACTIONp_mcangle_it3.022
X-RAY DIFFRACTIONp_scbond_it4.62
X-RAY DIFFRACTIONp_scangle_it6.63
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr0.170.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.260.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor19.615
X-RAY DIFFRACTIONp_orthonormal_tor23.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Lowest resolution: 7 Å / Rfactor obs: 0.177 / Highest resolution: 2.5 Å / Num. reflection all: 53315
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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