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

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Basic information

Entry
Database: PDB / ID: 4lnf
TitleB. subtilis glutamine synthetase structures reveal large active site conformational changes and basis for isoenzyme specific regulation: structure of GS-Q
ComponentsGlutamine synthetase
KeywordsLIGASE / glutamine synthetase / GS / enzyme / alpha-beta / TnrA / GlnR-DNA
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 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / 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 / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Creatine Kinase; Chain A, domain 2 / 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 / PHOSPHATE ION / Glutamine synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.949 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_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.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

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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)605,49164
Polymers602,48312
Non-polymers3,00952
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area69290 Å2
ΔGint-513 kcal/mol
Surface area177330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.000, 137.500, 137.700
Angle α, β, γ (deg.)119.80, 90.30, 93.40
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.: 36 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 40% MPD, 0.2 M magnesium chloride, pH 7.5, 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 24, 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: 2.949→119.014 Å / Num. all: 150000 / Num. obs: 143849 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 1.9 % / Rsym value: 0.11 / Net I/σ(I): 7
Reflection shellResolution: 2.949→3.11 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.373 / % possible all: 96.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LNN

4lnn


Resolution: 2.949→119.014 Å / SU ML: 0.37 / σ(F): 1.97 / Phase error: 26.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 11503 1.41 %RANDOM
Rwork0.1941 ---
all0.201 150000 --
obs0.195 143849 95.98 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.834 Å2 / ksol: 0.327 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-19.0618 Å21.1417 Å20.0757 Å2
2---13.8733 Å23.975 Å2
3----5.1885 Å2
Refinement stepCycle: LAST / Resolution: 2.949→119.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42406 0 165 253 42824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02243640
X-RAY DIFFRACTIONf_angle_d1.12459062
X-RAY DIFFRACTIONf_dihedral_angle_d19.57516280
X-RAY DIFFRACTIONf_chiral_restr0.0716360
X-RAY DIFFRACTIONf_plane_restr0.0057760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.949-3.05440.3562010.302914076X-RAY DIFFRACTION95
3.0544-3.17670.34392040.28314178X-RAY DIFFRACTION96
3.1767-3.32130.3141960.243114241X-RAY DIFFRACTION96
3.3213-3.49640.29422300.207314206X-RAY DIFFRACTION96
3.4964-3.71540.23432070.185714291X-RAY DIFFRACTION96
3.7154-4.00230.24611860.174514223X-RAY DIFFRACTION96
4.0023-4.40510.24071990.161314257X-RAY DIFFRACTION96
4.4051-5.04260.18382240.143114209X-RAY DIFFRACTION96
5.0426-6.35310.241940.183514136X-RAY DIFFRACTION96
6.3531-119.11070.29851830.197514008X-RAY DIFFRACTION95

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