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- PDB-6jtq: RVD HA specifically contacts 5mC through van der Waals interactions -

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Basic information

Entry
Database: PDB / ID: 6jtq
TitleRVD HA specifically contacts 5mC through van der Waals interactions
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
  • TAL effector
KeywordsDNA BINDING PROTEIN/DNA / methylation TAL effector / DNA BINDING PROTEIN-DNA complex
Function / homology: / TAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLiu, L. / Yi, C.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China21825701 China
National Natural Science Foundation of China91740112 China
CitationJournal: To Be Published
Title: RVD HA specifically contacts 5mC through van der Waals interactions
Authors: Liu, L. / Yi, C.
History
DepositionApr 11, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAL effector
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
B: TAL effector
C: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,6136
Polymers124,6136
Non-polymers00
Water2,018112
1
A: TAL effector
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,3063
Polymers62,3063
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-55 kcal/mol
Surface area24370 Å2
MethodPISA
2
B: TAL effector
C: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
D: DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,3063
Polymers62,3063
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-57 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.786, 88.022, 89.349
Angle α, β, γ (deg.)90.00, 104.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TAL effector


Mass: 51876.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZD72*PLUS
#2: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')


Mass: 5110.309 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5319.477 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 8-10% PEG3350 (w/v), 10% ethanol, 0.1 M MES pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9793 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 39755 / % possible obs: 98.8 % / Redundancy: 3.5 % / Net I/σ(I): 2.03
Reflection shellResolution: 2.48→2.547 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.872 / SU B: 11.308 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 0.751 / ESU R Free: 0.345 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28338 2095 5 %RANDOM
Rwork0.21778 ---
obs0.22107 39755 91.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 46.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20.15 Å2
2---1.15 Å2-0 Å2
3---0.81 Å2
Refinement stepCycle: 1 / Resolution: 2.48→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7210 1382 0 112 8704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0188868
X-RAY DIFFRACTIONr_bond_other_d0.0020.028178
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.82812384
X-RAY DIFFRACTIONr_angle_other_deg1.207318792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.695992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.15425.912274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.028151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5031532
X-RAY DIFFRACTIONr_chiral_restr0.0960.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219322
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021866
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5584.5933974
X-RAY DIFFRACTIONr_mcbond_other3.5494.5873973
X-RAY DIFFRACTIONr_mcangle_it5.8526.8724964
X-RAY DIFFRACTIONr_mcangle_other5.8526.8794965
X-RAY DIFFRACTIONr_scbond_it3.424.764894
X-RAY DIFFRACTIONr_scbond_other3.4194.764895
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.587.0697421
X-RAY DIFFRACTIONr_long_range_B_refined10.19837.53810244
X-RAY DIFFRACTIONr_long_range_B_other10.20637.57910215
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.483→2.547 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 71 -
Rwork0.223 1558 -
obs--48.63 %

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