[English] 日本語
Yorodumi
- PDB-2hgs: HUMAN GLUTATHIONE SYNTHETASE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hgs
TitleHUMAN GLUTATHIONE SYNTHETASE
ComponentsPROTEIN (GLUTATHIONE SYNTHETASE)
KeywordsAMINE/CARBOXYLATE LIGASE / AMINE-CARBOXYLATE LIGASE complex
Function / homology
Function and homology information


Defective GSS causes GSS deficiency / glutathione synthase / glutathione synthase activity / Glutathione synthesis and recycling / glutathione binding / amino acid metabolic process / response to cadmium ion / nervous system development / response to oxidative stress / magnesium ion binding ...Defective GSS causes GSS deficiency / glutathione synthase / glutathione synthase activity / Glutathione synthesis and recycling / glutathione binding / amino acid metabolic process / response to cadmium ion / nervous system development / response to oxidative stress / magnesium ion binding / protein homodimerization activity / extracellular exosome / ATP binding / identical protein binding / cytosol
Similarity search - Function
Glutathione synthase lid domain / Dna Ligase; domain 1 - #80 / Glutathione Synthetase; Chain A, domain 3 / Glutathione Synthetase; Chain A, domain 3 / Glutathione synthase, substrate-binding domain superfamily, eukaryotic / Glutathione synthase, substrate-binding domain / Eukaryotic glutathione synthase / Glutathione synthase, alpha-helical / Glutathione synthase, substrate-binding domain superfamily / Glutathione synthase, N-terminal, eukaryotic ...Glutathione synthase lid domain / Dna Ligase; domain 1 - #80 / Glutathione Synthetase; Chain A, domain 3 / Glutathione Synthetase; Chain A, domain 3 / Glutathione synthase, substrate-binding domain superfamily, eukaryotic / Glutathione synthase, substrate-binding domain / Eukaryotic glutathione synthase / Glutathione synthase, alpha-helical / Glutathione synthase, substrate-binding domain superfamily / Glutathione synthase, N-terminal, eukaryotic / Glutathione synthase, C-terminal, eukaryotic / Glutathione synthase / Eukaryotic glutathione synthase, ATP binding domain / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GLUTATHIONE / Glutathione synthetase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsPolekhina, G. / Board, P. / Rossjohn, J. / Parker, M.W.
Citation
Journal: EMBO J. / Year: 1999
Title: Molecular basis of glutathione synthetase deficiency and a rare gene permutation event.
Authors: Polekhina, G. / Board, P.G. / Gali, R.R. / Rossjohn, J. / Parker, M.W.
#1: Journal: Biochem.J. / Year: 1995
Title: Sequencing and Expression of a Cdna for Human Glutathione Synthetase
Authors: Gali, R.R. / Board, P.G.
History
DepositionJan 4, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 22, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
A: PROTEIN (GLUTATHIONE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4197
Polymers52,4441
Non-polymers9756
Water4,143230
1
A: PROTEIN (GLUTATHIONE SYNTHETASE)
hetero molecules

A: PROTEIN (GLUTATHIONE SYNTHETASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,83814
Polymers104,8872
Non-polymers1,95112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)84.260, 84.260, 197.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein PROTEIN (GLUTATHIONE SYNTHETASE)


Mass: 52443.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: CDNA / Organ: BRAIN / Plasmid: PRG1 / Production host: Escherichia coli (E. coli) / Strain (production host): TG1 / References: UniProt: P48637, glutathione synthase

-
Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.2 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMTris-HCl1drop
210 mM1dropMgSO4
31 mMdithiothreitol1drop
40.1 mMATP1drop
53-5 mg/mlprotein1drop
6100 mMMES1reservoir
710 mMGSH1reservoir
85 mMEDTA1reservoir
90.1-0.2 M1reservoirMgSO4
109-12 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.037
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 40495 / % possible obs: 95.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.057
Reflection
*PLUS
Num. measured all: 201501
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.2 Å / % possible obs: 95.9 % / Rmerge(I) obs: 0.197 / Mean I/σ(I) obs: 1.7

-
Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MIR / Resolution: 2.1→20 Å / Cross valid method: THROUGOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.281 4113 10 %RANDOM
Rwork0.218 ---
obs-40495 95.9 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 59 230 3964
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.01
X-RAY DIFFRACTIONp_angle_d0.0370.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0740.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.218
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