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- PDB-4s0r: Structure of GS-TnrA complex -

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Basic information

Entry
Database: PDB / ID: 4s0r
TitleStructure of GS-TnrA complex
Components
  • Glutamine synthetase
  • TnrA peptide
KeywordsLigase / chaperone / glutamine synthesis / transcription regulation
Function / homology
Function and homology information


nitrogen catabolite activation of 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 / core promoter sequence-specific DNA binding ...nitrogen catabolite activation of 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 / core promoter sequence-specific DNA binding / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / magnesium ion binding / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain ...Glutamine synthetase class-I, adenylation site / Glutamine synthetase class-I adenylation site. / Glutamine synthetase, N-terminal domain / Glutamine synthetase type I / Glutamine synthetase/guanido kinase, catalytic domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / MerR HTH family regulatory protein / Creatine Kinase; Chain A, domain 2 / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / MerR-type HTH domain / 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 / Putative DNA-binding domain superfamily / Ubiquitin-like (UB roll) / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / Glutamine synthetase / HTH-type transcriptional regulator TnrA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsSchumacher, M.A. / Chinnam, N.G. / Cuthbert, B. / Tonthat, N.K.
CitationJournal: Genes Dev. / Year: 2015
Title: Structures of regulatory machinery reveal novel molecular mechanisms controlling B. subtilis nitrogen homeostasis.
Authors: Schumacher, M.A. / Chinnam, N.B. / Cuthbert, B. / Tonthat, N.K. / Whitfill, T.
History
DepositionJan 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
M: Glutamine synthetase
N: Glutamine synthetase
O: TnrA peptide
P: TnrA peptide
Q: TnrA peptide
R: TnrA peptide
S: TnrA peptide
T: TnrA peptide
U: TnrA peptide
V: TnrA peptide
W: TnrA peptide
X: TnrA peptide
Y: TnrA peptide
Z: TnrA peptide
1: TnrA peptide
2: TnrA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)738,43489
Polymers735,24628
Non-polymers3,18861
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)295.800, 295.800, 103.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

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


Mass: 50620.379 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: glnA, BSU17460 / Production host: Escherichia coli (E. coli) / References: UniProt: P12425, glutamine synthetase
#2: Protein/peptide
TnrA peptide


Mass: 1897.188 Da / Num. of mol.: 14 / Source method: obtained synthetically / References: UniProt: Q45666*PLUS
#3: Chemical
ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C5H10N2O3
#4: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 47 / Source method: obtained synthetically / Formula: Mg

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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: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 298 K / pH: 6.5
Details: 25% PEG 400, MES, pH 6.5, 5% PEG 8000, 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: Mar 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→147.9 Å / Num. obs: 118362 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→147.9 Å / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.284 14817 RANDOM
Rwork0.243 --
obs0.243 118262 -
all-126078 -
Refinement stepCycle: LAST / Resolution: 3.5→147.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms51379 0 176 0 51555

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