[English] 日本語
Yorodumi
- PDB-7cpr: glutamine synthetase from Drosophila -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cpr
Titleglutamine synthetase from Drosophila
ComponentsGlutamine synthetase 2 cytoplasmic
KeywordsLIGASE / complex
Function / homology
Function and homology information


Astrocytic Glutamate-Glutamine Uptake And Metabolism / : / Glutamate and glutamine metabolism / glutamate catabolic process / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / synapse assembly / ATP binding / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Glutamine synthetase 2 cytoplasmic
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsYin, H.S. / Chen, W.T.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109B0020I5 Taiwan
CitationJournal: Biomolecules / Year: 2020
Title: Structural Insight into the Contributions of the N-Terminus and Key Active-Site Residues to the Catalytic Efficiency of Glutamine Synthetase 2.
Authors: Chen, W.T. / Yang, H.Y. / Lin, C.Y. / Lee, Y.Z. / Ma, S.C. / Chen, W.C. / Yin, H.S.
History
DepositionAug 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamine synthetase 2 cytoplasmic
B: Glutamine synthetase 2 cytoplasmic
C: Glutamine synthetase 2 cytoplasmic
D: Glutamine synthetase 2 cytoplasmic
E: Glutamine synthetase 2 cytoplasmic
F: Glutamine synthetase 2 cytoplasmic
G: Glutamine synthetase 2 cytoplasmic
H: Glutamine synthetase 2 cytoplasmic
I: Glutamine synthetase 2 cytoplasmic
J: Glutamine synthetase 2 cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)415,63220
Polymers411,36010
Non-polymers4,27210
Water9,368520
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58090 Å2
ΔGint-190 kcal/mol
Surface area118380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.698, 102.919, 206.508
Angle α, β, γ (deg.)90.000, 120.090, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Glutamine synthetase 2 cytoplasmic / Glutamate--ammonia ligase 2


Mass: 41136.020 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Gs2, CG1743 / Production host: Escherichia coli (E. coli) / References: UniProt: P20478, glutamine synthetase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20 mM Tris-HCl, pH 7.9, 150 mM NaCl, 5mM MgCl2, 5 mM ATP, 1 mM sodium 2-mercaptoethanesulfonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→178.68 Å / Num. obs: 234758 / % possible obs: 98 % / Redundancy: 2.8 % / CC1/2: 1 / Net I/σ(I): 16.14
Reflection shellResolution: 2.12→2.2 Å / Num. unique obs: 234758 / CC1/2: 1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OJW

2ojw


Resolution: 2.12→178.68 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.125 / SU ML: 0.178 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 11244 4.9 %RANDOM
Rwork0.1977 ---
obs0.2001 216390 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 217.58 Å2 / Biso mean: 51.442 Å2 / Biso min: 18.85 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å2-0 Å20.71 Å2
2--0.9 Å20 Å2
3---0.03 Å2
Refinement stepCycle: final / Resolution: 2.12→178.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28783 0 54 520 29357
Biso mean--99.46 38.45 -
Num. residues----3658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01929561
X-RAY DIFFRACTIONr_bond_other_d0.0060.0227050
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.95240118
X-RAY DIFFRACTIONr_angle_other_deg0.925362394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.80153648
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.21123.8191469
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.919154756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.80715239
X-RAY DIFFRACTIONr_chiral_restr0.1050.24166
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02134047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026946
LS refinement shellResolution: 2.12→2.175 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 821 -
Rwork0.289 15837 -
all-16658 -
obs--95.77 %

+
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