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

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Basic information

Entry
Database: PDB / ID: 4lnn
TitleB. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: structure of apo form of GS
ComponentsGlutamine synthetase
KeywordsLIGASE / glutamine synthetase / enzyme / dodecamer / 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
Glutamine synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 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 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Sep 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_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
G: Glutamine synthetase
H: Glutamine synthetase
I: Glutamine synthetase
J: Glutamine synthetase
K: Glutamine synthetase
L: Glutamine synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)603,57142
Polymers602,48312
Non-polymers1,08830
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area67360 Å2
ΔGint-462 kcal/mol
Surface area182680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.990, 138.380, 138.740
Angle α, β, γ (deg.)119.80, 90.19, 93.85
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 50206.906 Da / Num. of mol.: 12
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
#2: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 40 mg/mL protein, 40% MPD, 200 mM magnesium chloride/sulfate, pH 8.0, 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 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 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
ReflectionResolution: 3.1→120 Å / Num. all: 128448 / Num. obs: 110080 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

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

2bvc


Resolution: 3.1→84.25 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1907510.52 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 8288 7.5 %RANDOM
Rwork0.217 ---
obs0.217 110080 85.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.5518 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 66.5 Å2
Baniso -1Baniso -2Baniso -3
1-17.9 Å2-0.25 Å20.2 Å2
2---9.63 Å2-0.79 Å2
3----8.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.83 Å0.75 Å
Refinement stepCycle: LAST / Resolution: 3.1→84.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms41981 0 50 253 42284
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.472
X-RAY DIFFRACTIONc_scbond_it1.482
X-RAY DIFFRACTIONc_scangle_it2.522.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.382 984 7.5 %
Rwork0.36 12158 -
obs--61.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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