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- PDB-6uxz: (S)-4-Amino-5-phenoxypentanoate as a Selective Agonist of the Tra... -

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Basic information

Entry
Database: PDB / ID: 6uxz
Title(S)-4-Amino-5-phenoxypentanoate as a Selective Agonist of the Transcription Factor GabR
ComponentsHTH-type transcriptional regulatory protein GabR
KeywordsTRANSCRIPTION / GabR Transcription Factor / Selective agonist GABA. Metabolism
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 / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Chem-QL4 / HTH-type transcriptional regulatory protein GabR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCatlin, D.S. / Liu, D.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R15GM113229 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)R01 DA030604 United States
National Science Foundation (NSF, United States)ECCS-1542205 United States
CitationJournal: Protein Sci. / Year: 2020
Title: (S)-4-Amino-5-phenoxypentanoate designed as a potential selective agonist of the bacterial transcription factor GabR.
Authors: Catlin, D.S. / Reidl, C.T. / Trzupek, T.R. / Silverman, R.B. / Cannon, B.L. / Becker, D.P. / Liu, D.
History
DepositionNov 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,26910
Polymers83,8162
Non-polymers1,4538
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: fluorescence resonance energy transfer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint-91 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.650, 152.650, 69.160
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HTH-type transcriptional regulatory protein GabR


Mass: 41907.996 Da / Num. of mol.: 2
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: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-QL4 / (4S)-4-[(E)-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)amino]-5-phenoxypentanoic acid


Mass: 438.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N2O8P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 3350, 100 mM imidazole pH 8.0, and 200 mM Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 20715 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.2
Reflection shellResolution: 2.8→2.95 Å / Num. unique obs: 3701 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0189refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4T4J

4t4j


Resolution: 2.8→40 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.908 / SU B: 17.202 / SU ML: 0.332 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.412
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2631 1034 5 %RANDOM
Rwork0.1991 ---
obs0.2023 19629 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 169.65 Å2 / Biso mean: 70.315 Å2 / Biso min: 29.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.59 Å20 Å2
3---1.18 Å2
Refinement stepCycle: final / Resolution: 2.8→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5763 0 90 0 5853
Biso mean--82.14 --
Num. residues----717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196050
X-RAY DIFFRACTIONr_bond_other_d0.0020.025662
X-RAY DIFFRACTIONr_angle_refined_deg1.6331.9838174
X-RAY DIFFRACTIONr_angle_other_deg1.022313148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1565741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27123.357280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.864151117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5291552
X-RAY DIFFRACTIONr_chiral_restr0.0840.2895
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026603
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021259
LS refinement shellResolution: 2.8→2.873 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 69 -
Rwork0.351 1423 -
all-1492 -
obs--100 %

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