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- PDB-6xtv: FULL-LENGTH LTTR LYSG FROM CORYNEBACTERIUM GLUTAMICUM WITH BOUND ... -

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Basic information

Entry
Database: PDB / ID: 6xtv
TitleFULL-LENGTH LTTR LYSG FROM CORYNEBACTERIUM GLUTAMICUM WITH BOUND EFFECTOR ARG
ComponentsLysine export transcriptional regulatory protein LysG
KeywordsTRANSCRIPTION / LTTR HELIX-TURN-HELIX TRANSCRIPTION REGULATION
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
HTH-type transcriptional regulator ArgP / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ARGININE / Lysine export transcriptional regulatory protein LysG
Similarity search - Component
Biological speciesCorynebacterium glutamicum MB001 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å
AuthorsHofmann, E. / Syberg, F. / Schlicker, C. / Eggeling, L. / Schendzielorz, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchFlexFit Germany
Citation
Journal: Nat Commun / Year: 2020
Title: Engineering and application of a biosensor with focused ligand specificity.
Authors: Della Corte, D. / van Beek, H.L. / Syberg, F. / Schallmey, M. / Tobola, F. / Cormann, K.U. / Schlicker, C. / Baumann, P.T. / Krumbach, K. / Sokolowsky, S. / Morris, C.J. / Grunberger, A. / ...Authors: Della Corte, D. / van Beek, H.L. / Syberg, F. / Schallmey, M. / Tobola, F. / Cormann, K.U. / Schlicker, C. / Baumann, P.T. / Krumbach, K. / Sokolowsky, S. / Morris, C.J. / Grunberger, A. / Hofmann, E. / Schroder, G.F. / Marienhagen, J.
History
DepositionJan 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysine export transcriptional regulatory protein LysG
B: Lysine export transcriptional regulatory protein LysG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,0213
Polymers62,8462
Non-polymers1751
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-22 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.950, 123.950, 111.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Lysine export transcriptional regulatory protein LysG


Mass: 31423.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum MB001 (bacteria)
Gene: lysG, Cgl1263, cg1425 / Production host: Escherichia coli (E. coli) / References: UniProt: P94632
#2: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M SODIUM CHLORIDE; 0.1 M TRIS PH REMARK 280 8.5, 30 %(V/V) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979657 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979657 Å / Relative weight: 1
ReflectionResolution: 3→47 Å / Num. obs: 17846 / % possible obs: 99.65 % / Redundancy: 7.2 % / Biso Wilson estimate: 86.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1299 / Rpim(I) all: 0.05121 / Rrim(I) all: 0.1399 / Net I/σ(I): 15.77
Reflection shellResolution: 3→3.111 Å / Rmerge(I) obs: 1.94 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 12966 / CC1/2: 0.428 / Rpim(I) all: 0.7546 / Rrim(I) all: 2.084

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSVERSION Oct 15, 2015data reduction
XSCALEVERSION Oct 15, 2015 BUILT=20151231data scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6XTU

6xtu


Resolution: 3.3→47 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 --random
Rwork0.2065 ---
obs-17829 99.65 %-
Displacement parametersBiso mean: 92.26 Å2
Refinement stepCycle: LAST / Resolution: 3.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4371 0 12 0 4383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484459
X-RAY DIFFRACTIONf_angle_d0.85536064
X-RAY DIFFRACTIONf_chiral_restr0.0492712
X-RAY DIFFRACTIONf_plane_restr0.0063789
X-RAY DIFFRACTIONf_dihedral_angle_d14.33591663

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