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- PDB-5t4j: PLP and GABA Trigger GabR-Mediated Transcription Regulation in Ba... -

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Basic information

Entry
Database: PDB / ID: 5t4j
TitlePLP and GABA Trigger GabR-Mediated Transcription Regulation in Bacillus subsidies via External Aldimine Formation
ComponentsHTH-type transcriptional regulatory protein GabR
KeywordsTRANSCRIPTION REGULATOR / GabR / MocR / PLP / GABA / external aldimine
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: 2.231 Å
AuthorsWu, R. / Sanishvili, R. / Belitsky, B.R. / Juncosa, J.I. / Le, H.V. / Lehrer, H.J.S. / Farley, M. / Silverman, R.B. / Petsko, G.A. / Ringe, D. / Liu, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R15GM113229-01 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: PLP and GABA trigger GabR-mediated transcription regulation in Bacillus subtilis via external aldimine formation.
Authors: Wu, R. / Sanishvili, R. / Belitsky, B.R. / Juncosa, J.I. / Le, H.V. / Lehrer, H.J. / Farley, M. / Silverman, R.B. / Petsko, G.A. / Ringe, D. / Liu, D.
History
DepositionAug 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,2673
Polymers41,9171
Non-polymers3502
Water2,450136
1
B: HTH-type transcriptional regulatory protein GabR
hetero molecules

B: HTH-type transcriptional regulatory protein GabR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,5356
Polymers83,8342
Non-polymers7014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5840 Å2
ΔGint-25 kcal/mol
Surface area28150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.364, 128.894, 65.096
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-616-

HOH

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Components

#1: Protein HTH-type transcriptional regulatory protein GabR


Mass: 41917.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: gabR / Production host: Escherichia coli (E. coli) / References: UniProt: P94426
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-ABU / GAMMA-AMINO-BUTANOIC ACID / GAMMA(AMINO)-BUTYRIC ACID / Γ-Aminobutyric acid


Mass: 103.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO2 / Comment: neurotransmitter, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M Tris (pH:8.5) and 20% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-BM-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.23→49.2 Å / Num. obs: 104767 / % possible obs: 99.8 % / Redundancy: 5.5 % / Net I/σ(I): 29.3

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Processing

Software
NameVersionClassification
PHENIXdev_1563refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MGR

4mgr


Resolution: 2.231→49.183 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 20.62
RfactorNum. reflection% reflection
Rfree0.2107 977 5.1 %
Rwork0.1724 --
obs0.1744 19152 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.231→49.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2890 0 22 136 3048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053007
X-RAY DIFFRACTIONf_angle_d0.8624061
X-RAY DIFFRACTIONf_dihedral_angle_d15.461157
X-RAY DIFFRACTIONf_chiral_restr0.036444
X-RAY DIFFRACTIONf_plane_restr0.003521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2309-2.34850.23851210.19372463X-RAY DIFFRACTION95
2.3485-2.49560.26341420.18892577X-RAY DIFFRACTION100
2.4956-2.68830.24321630.19072557X-RAY DIFFRACTION100
2.6883-2.95880.22321300.18822607X-RAY DIFFRACTION100
2.9588-3.38690.25671450.1842604X-RAY DIFFRACTION100
3.3869-4.26670.20021420.16042635X-RAY DIFFRACTION100
4.2667-49.1950.1681340.15872732X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.63120.4484-0.33610.5651-0.71981.0976-0.01240.03290.0070.0434-0.14410.0403-0.13480.02510.18340.3721-0.00110.0470.3022-0.0040.3748-8.9202-5.3852.8066
21.96040.9023-0.6471.5276-0.65991.9684-0.02380.1443-0.086-0.08590.01860.21850.245-0.3099-0.01390.2615-0.03150.01420.3384-0.07590.3264-31.2849-14.93892.6157
31.25230.7855-0.62041.8631-0.52591.8416-0.0520.1821-0.1344-0.1906-0.03130.09710.3277-0.33990.08030.2999-0.03380.01550.355-0.10810.3033-27.8928-18.86781.1349
40.691-0.1521-0.48731.6187-1.35194.5721-0.08010.0833-0.1219-0.1413-0.1695-0.16060.69620.40060.19090.2702-0.0150.02880.2574-0.02660.312-8.2155-17.897110.3175
52.1251-0.58070.67021.8930.52873.1705-0.0058-0.28240.02610.2753-0.08220.16410.0084-0.34070.06760.3427-0.04950.08310.2662-0.02970.306-22.8679-14.711527.5949
66.56050.605-1.9133.3945-0.70194.05650.1715-0.5464-0.10890.5536-0.264-0.1728-0.22830.4908-0.03790.4344-0.09720.02730.344-0.00030.2598-12.7309-13.459234.0772
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 107 through 151 )
2X-RAY DIFFRACTION2chain 'B' and (resid 152 through 237 )
3X-RAY DIFFRACTION3chain 'B' and (resid 238 through 344 )
4X-RAY DIFFRACTION4chain 'B' and (resid 345 through 385 )
5X-RAY DIFFRACTION5chain 'B' and (resid 386 through 453 )
6X-RAY DIFFRACTION6chain 'B' and (resid 454 through 471 )

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