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- PDB-5x03: Crystal structure of the C-terminal domain of Bacillus subtilis G... -

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Basic information

Entry
Database: PDB / ID: 5x03
TitleCrystal structure of the C-terminal domain of Bacillus subtilis GabR reveals a closed conformation by the binding of gamma-aminobutyric acid, inducing the transcriptional activation
Components(HTH-type transcriptional regulatory protein GabR) x 2
KeywordsTRANSCRIPTION / Transcriptional regulator / Aminotransferase-like domain / External Schiff base
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase ...GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GAMMA-AMINO-BUTANOIC ACID / PYRIDOXAL-5'-PHOSPHATE / HTH-type transcriptional regulatory protein GabR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPark, S.A. / Lee, K.S.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2017
Title: Crystal structure of the C-terminal domain of Bacillus subtilis GabR reveals a closed conformation by gamma-aminobutyric acid binding, inducing transcriptional activation
Authors: Park, S.A. / Park, Y.S. / Lee, K.S.
History
DepositionJan 19, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulatory protein GabR
B: HTH-type transcriptional regulatory protein GabR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5335
Polymers83,9352
Non-polymers5973
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-22 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.497, 118.497, 75.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein HTH-type transcriptional regulatory protein GabR


Mass: 41819.957 Da / Num. of mol.: 1 / Fragment: UNP residues 108-470
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: gabR, ycnF, BSU03890 / Production host: Escherichia coli (E. coli) / References: UniProt: P94426
#2: Protein HTH-type transcriptional regulatory protein GabR


Mass: 42115.301 Da / Num. of mol.: 1 / Fragment: UNP residues 108-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: gabR, ycnF, BSU03890 / Production host: Escherichia coli (E. coli) / References: UniProt: P94426
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 3.17 Å3/Da / Density % sol: 61.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.1M HEPES pH 7.5, 1.5%(w/v) polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 69052 / % possible obs: 96.5 % / Redundancy: 4.6 % / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→37.472 Å / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 29.52
RfactorNum. reflection% reflection
Rfree0.2156 1979 2.88 %
Rwork0.1728 --
obs0.1741 68646 96.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→37.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5891 0 37 248 6176
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096044
X-RAY DIFFRACTIONf_angle_d1.1268143
X-RAY DIFFRACTIONf_dihedral_angle_d17.4132325
X-RAY DIFFRACTIONf_chiral_restr0.076882
X-RAY DIFFRACTIONf_plane_restr0.0051047
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.05010.29341300.24794356X-RAY DIFFRACTION86
2.0501-2.10540.30311360.23454534X-RAY DIFFRACTION90
2.1054-2.16720.24831270.22334556X-RAY DIFFRACTION90
2.1672-2.23690.26581300.21134635X-RAY DIFFRACTION92
2.2369-2.31670.25651380.20224662X-RAY DIFFRACTION93
2.3167-2.40910.23111350.19854755X-RAY DIFFRACTION94
2.4091-2.51830.23431350.20214783X-RAY DIFFRACTION95
2.5183-2.65050.25111400.19994834X-RAY DIFFRACTION96
2.6505-2.81580.2231390.19264874X-RAY DIFFRACTION96
2.8158-3.03180.23291360.194877X-RAY DIFFRACTION97
3.0318-3.33440.19891420.1674905X-RAY DIFFRACTION97
3.3344-3.8110.19791490.14344939X-RAY DIFFRACTION97
3.811-4.77980.18161460.12824950X-RAY DIFFRACTION97
4.7798-15.91510.18651450.15054937X-RAY DIFFRACTION95

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