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- PDB-8vxl: Crystal Structure of the External Aldimine Complex of Pyridoxal-5... -

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Basic information

Entry
Database: PDB / ID: 8vxl
TitleCrystal Structure of the External Aldimine Complex of Pyridoxal-5'-Tetrazole and (S)-4-amino-5-phenoxypentanoate with the Bacillus subtilis GabR C-terminal Effector-binding and Oligomerization Domain
ComponentsHTH-type transcriptional regulatory protein GabR
KeywordsTRANSCRIPTION / MocR / GabR / PLP / Transcription Regulator
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding / DNA-binding transcription factor activity / DNA binding
Similarity search - Function
: / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / 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
: / LYSINE / PHOSPHATE ION / HTH-type transcriptional regulatory protein GabR
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsKaley, N.E. / Liveris, Z.J. / Becker, D.P. / Liu, D.
Funding support1items
OrganizationGrant numberCountry
Other government1R15GM113229-0
CitationJournal: Protein Sci. / Year: 2025
Title: Bioisosteric replacement of pyridoxal-5'-phosphate to pyridoxal-5'-tetrazole targeting Bacillus subtilis GabR.
Authors: Kaley, N.E. / Liveris, Z.J. / Moore, M. / Reidl, C.T. / Wawrzak, Z. / Becker, D.P. / Liu, D.
History
DepositionFeb 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)90,10012
Polymers88,4052
Non-polymers1,69510
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-31 kcal/mol
Surface area28660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.319, 118.319, 75.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein HTH-type transcriptional regulatory protein GabR


Mass: 44202.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: gabR, ycnF, BSU03890 / Plasmid: pETite C-His / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P94426

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Non-polymers , 5 types, 130 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-A1AEJ / (4S)-4-[(E)-({3-hydroxy-2-methyl-5-[(E)-2-(1H-tetrazol-5-yl)ethenyl]pyridin-4-yl}methylidene)amino]-5-phenoxypentanoic acid


Mass: 422.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H22N6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 3% PEG 6000, 100mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12718 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12718 Å / Relative weight: 1
ReflectionResolution: 2.24→39.44 Å / Num. obs: 49997 / % possible obs: 99.71 % / Redundancy: 8.8 % / Biso Wilson estimate: 37.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.052 / Rrim(I) all: 0.158 / Net I/σ(I): 11.1
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 5 % / Rmerge(I) obs: 1.068 / Mean I/σ(I) obs: 1 / Num. unique obs: 2397 / CC1/2: 0.536 / Rpim(I) all: 0.529 / Rrim(I) all: 1.197 / % possible all: 98.38

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→39.44 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2556 2535 5.07 %
Rwork0.2126 --
obs0.2145 49997 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.24→39.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5763 0 111 120 5994
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096024
X-RAY DIFFRACTIONf_angle_d1.0438126
X-RAY DIFFRACTIONf_dihedral_angle_d8.579830
X-RAY DIFFRACTIONf_chiral_restr0.056893
X-RAY DIFFRACTIONf_plane_restr0.0111042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.280.34021620.30062525X-RAY DIFFRACTION98.38
2.28-2.330.29911380.29092623X-RAY DIFFRACTION100
2.33-2.380.34671400.27812614X-RAY DIFFRACTION100
2.38-2.440.32191560.26572580X-RAY DIFFRACTION100
2.44-2.50.2821490.26762674X-RAY DIFFRACTION100
2.5-2.560.30451450.2592569X-RAY DIFFRACTION100
2.56-2.640.32251200.2572664X-RAY DIFFRACTION100
2.64-2.720.29281610.25312619X-RAY DIFFRACTION100
2.73-2.820.27241510.25832636X-RAY DIFFRACTION100
2.82-2.940.30621510.25912589X-RAY DIFFRACTION100
2.94-3.070.26361470.24972638X-RAY DIFFRACTION100
3.07-3.230.25431440.21962665X-RAY DIFFRACTION100
3.23-3.430.26861320.21962622X-RAY DIFFRACTION100
3.43-3.70.26221190.19792678X-RAY DIFFRACTION100
3.7-4.070.19881240.1892668X-RAY DIFFRACTION100
4.07-4.660.22611410.16582668X-RAY DIFFRACTION100
4.66-5.870.21451410.1782670X-RAY DIFFRACTION100
5.87-39.440.21311140.1732732X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -58.6125 Å / Origin y: 22.9284 Å / Origin z: 20.0718 Å
111213212223313233
T0.245 Å20.0054 Å2-0.0392 Å2-0.1955 Å20.0051 Å2--0.2891 Å2
L0.8157 °20.1505 °2-0.3269 °2-0.9901 °20.0841 °2--1.1052 °2
S-0.1714 Å °-0.0134 Å °-0.0415 Å °-0.0161 Å °0.1553 Å °-0.0066 Å °-0.0014 Å °0.0541 Å °0.0357 Å °
Refinement TLS groupSelection details: all

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