[English] 日本語
Yorodumi
- PDB-2uu7: Crystal structure of apo glutamine synthetase from dog (Canis fam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uu7
TitleCrystal structure of apo glutamine synthetase from dog (Canis familiaris)
ComponentsGLUTAMINE SYNTHETASE
KeywordsLIGASE
Function / homology
Function and homology information


protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / angiogenesis / endoplasmic reticulum ...protein S-acyltransferase / protein palmitoylation / protein-cysteine S-palmitoyltransferase activity / regulation of sprouting angiogenesis / regulation of endothelial cell migration / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / angiogenesis / endoplasmic reticulum / mitochondrion / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. ...: / Glutamine synthetase, N-terminal domain / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesCANIS FAMILIARIS (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKrajewski, W.W. / Jones, T.A. / Mowbray, S.L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal Structures of Mammalian Glutamine Synthetases Illustrate Substrate-Induced Conformational Changes and Provide Opportunities for Drug and Herbicide Design.
Authors: Krajewski, W.W. / Collins, R. / Holmberg-Schiavone, L. / Jones, T.A. / Karlberg, T. / Mowbray, S.L.
History
DepositionFeb 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTAMINE SYNTHETASE
B: GLUTAMINE SYNTHETASE
C: GLUTAMINE SYNTHETASE
D: GLUTAMINE SYNTHETASE
E: GLUTAMINE SYNTHETASE
F: GLUTAMINE SYNTHETASE
G: GLUTAMINE SYNTHETASE
H: GLUTAMINE SYNTHETASE
I: GLUTAMINE SYNTHETASE
J: GLUTAMINE SYNTHETASE
K: GLUTAMINE SYNTHETASE
L: GLUTAMINE SYNTHETASE
M: GLUTAMINE SYNTHETASE
N: GLUTAMINE SYNTHETASE
O: GLUTAMINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)648,19845
Polymers647,30215
Non-polymers89630
Water00
1
A: GLUTAMINE SYNTHETASE
B: GLUTAMINE SYNTHETASE
C: GLUTAMINE SYNTHETASE
D: GLUTAMINE SYNTHETASE
E: GLUTAMINE SYNTHETASE
F: GLUTAMINE SYNTHETASE
G: GLUTAMINE SYNTHETASE
H: GLUTAMINE SYNTHETASE
I: GLUTAMINE SYNTHETASE
J: GLUTAMINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,13230
Polymers431,53410
Non-polymers59820
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area48950 Å2
ΔGint-237 kcal/mol
Surface area160270 Å2
MethodPQS
2
K: GLUTAMINE SYNTHETASE
L: GLUTAMINE SYNTHETASE
M: GLUTAMINE SYNTHETASE
N: GLUTAMINE SYNTHETASE
O: GLUTAMINE SYNTHETASE
hetero molecules

K: GLUTAMINE SYNTHETASE
L: GLUTAMINE SYNTHETASE
M: GLUTAMINE SYNTHETASE
N: GLUTAMINE SYNTHETASE
O: GLUTAMINE SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)432,13230
Polymers431,53410
Non-polymers59820
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area54040 Å2
ΔGint-257.1 kcal/mol
Surface area160280 Å2
MethodPQS
Unit cell
Length a, b, c (Å)183.590, 485.602, 192.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 500
2111B3 - 500
3111C3 - 500
4111D3 - 500
5111E3 - 500
6111F3 - 500
7111G3 - 500
8111H3 - 500
9111I3 - 500
10111J3 - 500
11111K3 - 500
12111L3 - 500
13111M3 - 500
14111N3 - 500
15111O3 - 500

NCS oper:
IDCodeMatrixVector
1given(0.30839, 0.009611, 0.951211), (0.080855, 0.996065, -0.036278), (-0.947817, 0.088098, 0.3064)27.30328, -2.68032, 28.67525
2given(-0.804349, 0.089814, 0.58733), (0.144215, 0.98846, 0.046348), (-0.57639, 0.121982, -0.808019)63.82787, -4.52986, 9.01381
3given(-0.802277, 0.134165, -0.58168), (0.072441, 0.989096, 0.128223), (0.592541, 0.060733, -0.803248)58.53264, -1.54064, -32.18757
4given(0.31078, 0.078438, -0.94724), (-0.012399, 0.996839, 0.078477), (0.950401, -0.012644, 0.310771)19.23977, 1.10542, -38.1184
5given(0.446656, -0.128672, 0.885405), (-0.132616, -0.988195, -0.076709), (0.884823, -0.083157, -0.458447)43.48824, 327.57129, -22.571
6given(-0.707465, -0.053981, 0.704684), (-0.047005, -0.991277, -0.123126), (0.705183, -0.120231, 0.698757)82.3733, 324.32779, -10.64501
7given(-0.889698, -0.004699, -0.456526), (0.034176, -0.997827, -0.056332), (-0.455269, -0.065721, 0.887925)84.40288, 321.54889, 31.07947
8given(0.147494, -0.035618, -0.988421), (-0.014022, -0.999326, 0.033919), (-0.988964, 0.008857, -0.147894)45.07067, 323.84741, 44.06144
9given(0.981417, -0.110124, -0.157143), (-0.108497, -0.993917, 0.018921), (-0.15827, -0.00152, -0.987395)18.98172, 327.11673, 10.7819
10given(-0.995567, 0.055376, 0.076031), (0.061527, 0.994806, 0.081092), (-0.071146, 0.085411, -0.993802)82.50835, 79.1162, 87.07421
11given(-0.378121, 0.058682, -0.923895), (0.018747, 0.99827, 0.055734), (0.925566, 0.003754, -0.378567)56.59372, 80.57099, 55.61307
12given(0.762318, -0.015546, -0.647017), (0.027382, 0.999591, 0.008245), (0.646624, -0.024002, 0.762431)18.04815, 80.15544, 70.42603
13given(0.849393, -0.069523, 0.523162), (0.07635, 0.997045, 0.008537), (-0.522209, 0.032692, 0.852191)20.83094, 78.36236, 112.1718
14given(-0.233876, -0.027314, 0.971883), (0.083954, 0.995305, 0.048175), (-0.968635, 0.09286, -0.230485)60.71241, 78.35348, 123.6545

-
Components

#1: Protein
GLUTAMINE SYNTHETASE / GLUTAMATE--AMMONIA LIGASE / GS


Mass: 43153.438 Da / Num. of mol.: 15
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANIS FAMILIARIS (dog) / Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21STAR(DE3) / References: UniProt: Q8HZM5, glutamine synthetase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.6 % / Description: NONE
Crystal growpH: 8.5 / Details: 15% PEG3350, 0.2 M POTASSIUM CITRATE, pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9765
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 168869 / % possible obs: 99 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.5
Reflection shellResolution: 3→3.16 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 3.3 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D3A

2d3a


Resolution: 3→29.99 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.896 / SU B: 15.164 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.357 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2015 1.2 %RANDOM
Rwork0.213 ---
obs0.213 166824 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.43 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20 Å2
2---1.97 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 3→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43995 0 30 0 44025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02245210
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9461125
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.89955535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.26823.6842280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.079157395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.64115330
X-RAY DIFFRACTIONr_chiral_restr0.0950.26105
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0235685
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.219460
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.231028
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.21201
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5390.2154
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5430.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3381.527992
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.487244220
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.32319433
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.94.516905
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 2934 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Btight positional0.040.05
3Ctight positional0.040.05
4Dtight positional0.040.05
5Etight positional0.040.05
6Ftight positional0.040.05
7Gtight positional0.040.05
8Htight positional0.050.05
9Itight positional0.040.05
10Jtight positional0.040.05
11Ktight positional0.040.05
12Ltight positional0.050.05
13Mtight positional0.040.05
14Ntight positional0.040.05
15Otight positional0.040.05
1Atight thermal0.080.5
2Btight thermal0.080.5
3Ctight thermal0.080.5
4Dtight thermal0.080.5
5Etight thermal0.080.5
6Ftight thermal0.090.5
7Gtight thermal0.090.5
8Htight thermal0.090.5
9Itight thermal0.080.5
10Jtight thermal0.080.5
11Ktight thermal0.080.5
12Ltight thermal0.080.5
13Mtight thermal0.080.5
14Ntight thermal0.10.5
15Otight thermal0.090.5
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.312 156
Rwork0.321 12053

+
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