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- PDB-6lg2: VanR bound to Vanillate -

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Basic information

Entry
Database: PDB / ID: 6lg2
TitleVanR bound to Vanillate
ComponentsPredicted transcriptional regulators
KeywordsTRANSCRIPTION / VanR transcription factor Vanillate
Function / homologyTranscription regulator PadR, N-terminal / Transcriptional regulator PadR-like family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 4-HYDROXY-3-METHOXYBENZOATE / Predicted transcriptional regulators
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHe, Y. / Bharath, S.R. / Song, H.
CitationJournal: Nat Commun / Year: 2020
Title: Developing a highly efficient hydroxytyrosol whole-cell catalyst by de-bottlenecking rate-limiting steps.
Authors: Yao, J. / He, Y. / Su, N. / Bharath, S.R. / Tao, Y. / Jin, J.M. / Chen, W. / Song, H. / Tang, S.Y.
History
DepositionDec 4, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Predicted transcriptional regulators
B: Predicted transcriptional regulators
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5194
Polymers43,1852
Non-polymers3342
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-43 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.974, 83.559, 63.278
Angle α, β, γ (deg.)90.000, 92.217, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Predicted transcriptional regulators


Mass: 21592.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: vanR transcriptional regulator
Source: (gene. exp.) Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025) (bacteria)
Strain: ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025
Gene: Cgl2382 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NN31
#2: Chemical ChemComp-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate


Mass: 167.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H7O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride 0.1 M Tris pH 8.0 12% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→29.57 Å / Num. obs: 44461 / % possible obs: 93 % / Redundancy: 1.8 % / Biso Wilson estimate: 15.22 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.3
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2195 / CC1/2: 0.434

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L9F

3l9f


Resolution: 1.6→29.57 Å / SU ML: 0.1921 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.0677
RfactorNum. reflection% reflection
Rfree0.2377 2253 5.07 %
Rwork0.1909 --
obs0.1933 44437 92.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.32 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 24 335 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00593008
X-RAY DIFFRACTIONf_angle_d0.77174065
X-RAY DIFFRACTIONf_chiral_restr0.0455437
X-RAY DIFFRACTIONf_plane_restr0.0059521
X-RAY DIFFRACTIONf_dihedral_angle_d23.51521103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.32491430.27892612X-RAY DIFFRACTION92.64
1.63-1.670.28761160.26722645X-RAY DIFFRACTION92.37
1.67-1.710.29891410.24742607X-RAY DIFFRACTION91.84
1.71-1.760.2791490.2412544X-RAY DIFFRACTION89.92
1.76-1.810.251290.23332484X-RAY DIFFRACTION88.19
1.81-1.870.26611030.21792518X-RAY DIFFRACTION88.16
1.87-1.940.25881510.20682619X-RAY DIFFRACTION91.97
1.94-2.020.26631460.19292648X-RAY DIFFRACTION94.01
2.02-2.110.23951460.18262662X-RAY DIFFRACTION93.88
2.11-2.220.20371650.16982651X-RAY DIFFRACTION94.46
2.22-2.360.26221100.17962733X-RAY DIFFRACTION94.55
2.36-2.540.22771460.18992656X-RAY DIFFRACTION93.4
2.54-2.790.22151560.18452660X-RAY DIFFRACTION94.62
2.79-3.20.211710.18822728X-RAY DIFFRACTION95.65
3.2-4.030.21521520.16452676X-RAY DIFFRACTION94.2
4.03-29.570.24551290.17872741X-RAY DIFFRACTION93.88

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