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

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Basic information

Entry
Database: PDB / ID: 6jvz
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 complex / DNA BINDING PROTEIN-DNA complex
Function / homologyTAL effector repeat / TAL effector repeat / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas campestris pv. armoraciae (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 China (NSFC)91953201 China
National Natural Science Foundation of China (NSFC)21825701 China
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Structural Insights into the Specific Recognition of 5-methylcytosine and 5-hydroxymethylcytosine by TAL Effectors.
Authors: Liu, L. / Zhang, Y. / Liu, M. / Wei, W. / Yi, C. / Peng, J.
History
DepositionApr 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
Water1,946108
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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6440 Å2
ΔGint-55 kcal/mol
Surface area24410 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 area6350 Å2
ΔGint-55 kcal/mol
Surface area26850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.786, 88.022, 89.349
Angle α, β, γ (deg.)90.000, 104.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12I
22C
13J
23D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETHISHISAA230 - 7261 - 497
21METMETHISHISBD230 - 7261 - 497
12DTDTDTDTIB-2 - 141 - 17
22DTDTDTDTCE-2 - 141 - 17
13DADADADAJC-14 - 21 - 17
23DADADADADF-14 - 21 - 17

NCS ensembles :
ID
1
2
3

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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 campestris pv. armoraciae (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.: 108 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 8-10% PEG3350 (w/v), 10% ethanol, and 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→86.4 Å / Num. obs: 39755 / % possible obs: 98.8 % / Redundancy: 3.5 % / Rrim(I) all: 0.096 / Net I/σ(I): 2.03
Reflection shellResolution: 2.48→2.52 Å / Rrim(I) all: 0.908

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GJP

4gjp


Resolution: 2.48→86.4 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.2 / SU ML: 0.252 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.771 / ESU R Free: 0.335
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 2095 5 %RANDOM
Rwork0.2233 ---
obs0.2259 39755 91.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 221.86 Å2 / Biso mean: 44.467 Å2 / Biso min: 11.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å20.18 Å2
2---1.11 Å2-0 Å2
3---0.87 Å2
Refinement stepCycle: final / Resolution: 2.48→86.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7215 1382 0 108 8705
Biso mean---27.93 -
Num. residues----1062
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0188874
X-RAY DIFFRACTIONr_bond_other_d0.0040.028183
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.82812392
X-RAY DIFFRACTIONr_angle_other_deg1.405318804
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.6445992
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.85725.891275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.558151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2811532
X-RAY DIFFRACTIONr_chiral_restr0.0930.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0219328
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021870
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A256310.17
12B256310.17
21I13190.13
22C13190.13
31J12350.13
32D12350.13
LS refinement shellResolution: 2.483→2.547 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 71 -
Rwork0.244 1558 -
all-1629 -
obs--48.63 %

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