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

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Basic information

Entry
Database: PDB / ID: 6lew
TitleRVD HA specifically contacts 5mC through van der Waals interactions
Components
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*CP*GP*TP*CP*TP*CP*T)-3')
  • DNA (5'-D(P*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • TAL effector
KeywordsDNA BINDING PROTEIN/DNA / methylation TAL effector complex / DNA BINDING PROTEIN-DNA complex
Function / homology: / TAL 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 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
DepositionNov 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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(P*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(P*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(P*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 area6250 Å2
ΔGint-56 kcal/mol
Surface area23550 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(P*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 area5980 Å2
ΔGint-52 kcal/mol
Surface area22360 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
11ARGARGLEULEUAA236 - 6887 - 459
21ARGARGSERSERBD236 - 6897 - 460
12DTDTDTDTIB-2 - 121 - 15
22DTDTDTDTCE-2 - 121 - 15
13DGDGDADAJC-13 - 22 - 17
23DGDGDADADF-13 - 22 - 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(P*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
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 0.1M MES pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / 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: 99.7 % / Redundancy: 3.6 % / Rrim(I) all: 0.096 / Net I/σ(I): 2.03
Reflection shellResolution: 2.48→4 Å / Num. unique obs: 39755 / Rrim(I) all: 0.096

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
PDB_EXTRACT3.25data extraction
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: 0.912 / Cor.coef. Fo:Fc free: 0.873 / SU B: 23.372 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.602 / ESU R Free: 0.324
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2786 2095 5 %RANDOM
Rwork0.2306 ---
obs0.233 39755 91.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.44 Å2 / Biso mean: 40.382 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20.73 Å2
2---2.59 Å2-0 Å2
3---1.52 Å2
Refinement stepCycle: final / Resolution: 2.48→86.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6526 1327 0 112 7965
Biso mean---29.82 -
Num. residues----968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0188083
X-RAY DIFFRACTIONr_bond_other_d0.0040.027487
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.82511266
X-RAY DIFFRACTIONr_angle_other_deg1.199317195
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3475882
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.24726.183241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.385151081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0341528
X-RAY DIFFRACTIONr_chiral_restr0.0810.21328
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218327
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021668
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A230170.13
12B230170.13
21I11930.12
22C11930.12
31J11950.11
32D11950.11
LS refinement shellResolution: 2.483→2.547 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 71 -
Rwork0.254 1558 -
all-1629 -
obs--48.63 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9349-0.1622-0.43090.8365-0.22891.37980.08370.17140.1315-0.13960.0373-0.1493-0.05460.1332-0.1210.1098-0.0082-0.02530.2015-0.02470.10112.158314.111440.561
22.99760.8571-2.08223.1314-0.52461.7070.26060.09720.1461-0.0288-0.0806-0.0681-0.25280.1037-0.180.0482-0.03350.02260.124-0.04120.08629.077116.919446.254
31.8915-0.0411-0.97822.0335-1.09857.20160.0630.19770.0809-0.0181-0.00450.09990.0169-0.1756-0.05850.0814-0.03160.00970.1415-0.02730.20988.0419.149747.9092
40.9356-0.0216-0.08021.39540.00721.2468-0.00870.1794-0.1966-0.10820.0247-0.10370.12780.1382-0.0160.06750.0055-0.04430.2532-0.05610.1096-23.93039.1615.3932
51.170.2239-1.06732.54330.0731.0196-0.10440.0016-0.0855-0.25930.0698-0.10290.09240.0550.03450.12590.0238-0.06650.2174-0.06710.0878-27.879112.69044.1563
66.5707-4.07152.07474.2889-0.74642.80750.02350.0481-0.09720.02520.0329-0.1048-0.01080.1369-0.05640.1537-0.0310.01360.20580.02530.1411-29.613212.69025.7509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A234 - 726
2X-RAY DIFFRACTION2I-2 - 14
3X-RAY DIFFRACTION3J-13 - 2
4X-RAY DIFFRACTION4B234 - 689
5X-RAY DIFFRACTION5C-2 - 13
6X-RAY DIFFRACTION6D-13 - 2

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