[English] 日本語
Yorodumi
- PDB-1a7k: GLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLIN... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a7k
TitleGLYCOSOMAL GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE IN A MONOCLINIC CRYSTAL FORM
ComponentsGLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GLYCOSOME / TRYPANOSOME
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / glycosome / 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 / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / Glyceraldehyde-3-phosphate dehydrogenase, glycosomal
Similarity search - Component
Biological speciesLeishmania mexicana (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKim, H. / Hol, W.G.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Crystal structure of Leishmania mexicana glycosomal glyceraldehyde-3-phosphate dehydrogenase in a new crystal form confirms the putative physiological active site structure.
Authors: Kim, H. / Hol, W.G.
#1: Journal: Biochemistry / Year: 1995
Title: Crystal Structure of Glycosomal Glyceraldehyde-3-Phosphate Dehydrogenase from Leishmania Mexicana: Implications for Structure-Based Drug Design and a New Position for the Inorganic Phosphate Binding Site
Authors: Kim, H. / Feil, I.K. / Verlinde, C.L. / Petra, P.H. / Hol, W.G.
History
DepositionMar 16, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
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)159,22716
Polymers155,8144
Non-polymers3,41312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22160 Å2
ΔGint-200 kcal/mol
Surface area45050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.900, 81.000, 131.900
Angle α, β, γ (deg.)90.00, 95.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999472, 0.030711, -0.010656), (0.027818, 0.638457, -0.769155), (-0.016818, -0.769044, -0.638974)
Vector: 93.23406, 107.34053, 232.33264)

-
Components

#1: Protein
GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE / GAPDH


Mass: 38953.504 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: ONE BOUND NAD AND TWO BOUND PHOSPHATES PER MONOMER / Source: (gene. exp.) Leishmania mexicana (eukaryote) / Cell line: BL21 / Plasmid: PET-3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 PLYSS
References: UniProt: Q27890, glyceraldehyde-3-phosphate dehydrogenase (phosphorylating)
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growMethod: vapor diffusion / pH: 7
Details: VAPOR DIFFUSION: 100 MM SODIUM PHOSPHATE, 27.5% PEG-1000 PH 7.0 (PH ADJUSTED WITH 100 MM CITRIC ACID), vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19 mg/mlprotein1drop
2100 mMtriethanolamine1drop
3200 mM1dropKCl
41 mMdithiothreitol1drop
51 mMEDTA1drop
6100 mMsodium phosphate1reservoir
727.5 %PEG10001reservoir
8100 mMcitric acid1reservoir

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.98
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 2, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 28710 / % possible obs: 81 % / Redundancy: 2.5 % / Biso Wilson estimate: 52 Å2 / Rsym value: 0.071
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.481 / % possible all: 81
Reflection
*PLUS
Num. measured all: 78266 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.481

-
Processing

Software
NameVersionClassification
X-PLOR3model building
X-PLOR3refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TRYPANOSOMA BRUCEI GAPDH

Resolution: 2.8→8 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.292 1343 5 %RANDOM
Rwork0.217 ---
obs0.217 27607 81 %-
Displacement parametersBiso mean: 49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10864 0 216 0 11080
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellHighest resolution: 2.8 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.42 150 4 %
Rwork0.338 3227 -
obs--80 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4
LS refinement shell
*PLUS
Rfactor obs: 0.338

+
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