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- PDB-4lnk: B. subtilis glutamine synthetase structures reveal large active s... -

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Basic information

Entry
Database: PDB / ID: 4lnk
TitleB. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: structure of GS-glutamate-AMPPCP complex
ComponentsGlutamine synthetase
KeywordsLIGASE / alpha-beta
Function / homology
Function and homology information


cellular response to nitrogen levels / glutamine binding / nitrogen catabolite repression of transcription / negative regulation of core promoter binding / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / glutamate binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription ...cellular response to nitrogen levels / glutamine binding / nitrogen catabolite repression of transcription / negative regulation of core promoter binding / glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / glutamate binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Glutamine synthetase, N-terminal domain / Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / 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, glycine-rich site ...Glutamine synthetase, N-terminal domain / Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase type I / 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, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / GLUTAMIC ACID / Glutamine synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsSchumacher, M.A. / Chinnam, N. / Tonthat, N. / Fisher, S. / Wray, L.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structures of the Bacillus subtilis Glutamine Synthetase Dodecamer Reveal Large Intersubunit Catalytic Conformational Changes Linked to a Unique Feedback Inhibition Mechanism.
Authors: Murray, D.S. / Chinnam, N. / Tonthat, N.K. / Whitfill, T. / Wray, L.V. / Fisher, S.H. / Schumacher, M.A.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2013Group: Database references
Revision 1.2Jan 15, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_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_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,26733
Polymers301,2416
Non-polymers4,02627
Water1,02757
1
A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
hetero molecules

A: Glutamine synthetase
B: Glutamine synthetase
C: Glutamine synthetase
D: Glutamine synthetase
E: Glutamine synthetase
F: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)610,53566
Polymers602,48312
Non-polymers8,05254
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area78280 Å2
ΔGint-559 kcal/mol
Surface area173910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.500, 240.860, 207.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 50206.906 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: glnA, BSU17460 / Production host: Escherichia coli (E. coli) / References: UniProt: P12425, glutamine synthetase

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Non-polymers , 5 types, 84 molecules

#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.3 %
Crystal growTemperature: 298 K / pH: 6.8
Details: 10% PEG, 15 mM magnesium chloride, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2012
RadiationMonochromator: KHOZU DOUBLE FLAT CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -1/2*h+1/2*k,3/2*h+1/2*k,-l / Fraction: 0.278
ReflectionResolution: 2.87→120.07 Å / Num. all: 72956 / Num. obs: 72956 / % possible obs: 91 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.11 / Net I/σ(I): 6
Reflection shellResolution: 2.87→3.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.528 / % possible all: 69.8

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
MOLREPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LNN

4lnn


Resolution: 2.87→120.065 Å / Isotropic thermal model: RESTRAINED / σ(F): 0 / Phase error: 34.89 / Stereochemistry target values: TWIN_LSQ_F / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflection
Rfree0.2356 11686 16.02 %
Rwork0.1948 --
obs0.1999 72956 91.79 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.248 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.7209 Å2-0 Å20 Å2
2---7.7672 Å2-0 Å2
3---14.488 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.87→120.065 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21210 0 247 57 21514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121946
X-RAY DIFFRACTIONf_angle_d1.32729732
X-RAY DIFFRACTIONf_dihedral_angle_d18.6768206
X-RAY DIFFRACTIONf_chiral_restr0.0773204
X-RAY DIFFRACTIONf_plane_restr0.0063886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8901-2.93990.4063190.36812216X-RAY DIFFRACTION58
2.9399-2.99340.35483520.32912338X-RAY DIFFRACTION61
2.9934-3.05090.32893670.29822525X-RAY DIFFRACTION65
3.0509-3.11320.32283730.28972639X-RAY DIFFRACTION69
3.1132-3.18090.31044200.27962780X-RAY DIFFRACTION72
3.1809-3.25480.33874440.27872954X-RAY DIFFRACTION77
3.2548-3.33620.29994970.25943220X-RAY DIFFRACTION83
3.3362-3.42640.27475330.24753332X-RAY DIFFRACTION86
3.4264-3.52720.26765290.2313327X-RAY DIFFRACTION86
3.5272-3.6410.25225220.2293344X-RAY DIFFRACTION86
3.641-3.7710.25965270.20973344X-RAY DIFFRACTION86
3.771-3.92190.25195610.20263298X-RAY DIFFRACTION85
3.9219-4.10030.22885250.18953360X-RAY DIFFRACTION86
4.1003-4.31630.20725160.1693357X-RAY DIFFRACTION86
4.3163-4.58650.20415340.15313334X-RAY DIFFRACTION86
4.5865-4.94030.18835030.1483391X-RAY DIFFRACTION87
4.9403-5.43670.19145340.14793355X-RAY DIFFRACTION86
5.4367-6.22170.24085280.19143351X-RAY DIFFRACTION85
6.2217-7.83220.24865110.18813378X-RAY DIFFRACTION85
7.8322-45.50410.17895280.14213433X-RAY DIFFRACTION84

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