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- PDB-3v6t: Crystal structure of the DNA-bound dHax3, a TAL effector, at 1.85... -

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Basic information

Entry
Database: PDB / ID: 3v6t
TitleCrystal structure of the DNA-bound dHax3, a TAL effector, at 1.85 angstrom
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
  • dHax3
KeywordsDNA BINDING PROTEIN/DNA / 11 tandem repeats / DNA specific binding protein / DNA BINDING PROTEIN-DNA complex
Function / homologyDNA / DNA (> 10)
Function and homology information
Biological speciesXanthomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDeng, D. / Yan, C.Y. / Pan, X.J. / Wang, J.W. / Yan, N. / Shi, Y.G.
CitationJournal: Science / Year: 2012
Title: Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors
Authors: Deng, D. / Yan, C.Y. / Pan, X.J. / Mahfouz, M. / Wang, J.W. / Zhu, J.K. / Shi, Y.G. / Yan, N.
History
DepositionDec 20, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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: dHax3
B: dHax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)124,2996
Polymers124,2996
Non-polymers00
Water18,8441046
1
A: dHax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,1493
Polymers62,1493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-61 kcal/mol
Surface area24030 Å2
MethodPISA
2
B: dHax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)62,1493
Polymers62,1493
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5340 Å2
ΔGint-59 kcal/mol
Surface area24830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.719, 87.679, 88.494
Angle α, β, γ (deg.)90.00, 103.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein dHax3


Mass: 51736.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas (bacteria) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3')


Mass: 5070.281 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5342.513 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1046 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.48 Å3/Da / Density % sol: 50.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 8-10% PEG 3350(w/v), 12% ethanol, 0.1M MES pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2011
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 103545 / Num. obs: 103239 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 25.05 Å2
Reflection shellResolution: 1.85→1.92 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3V6P

3v6p


Resolution: 1.85→32.316 Å / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.8393 / σ(F): 1.33 / Phase error: 23.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2217 5161 5 %RANDOM
Rwork0.2051 ---
all0.206 103545 --
obs0.206 103200 99.46 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.024 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso max: 127.28 Å2 / Biso mean: 32.0372 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.2195 Å20 Å2-1.3862 Å2
2--1.1124 Å2-0 Å2
3---1.2129 Å2
Refinement stepCycle: LAST / Resolution: 1.85→32.316 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7065 1381 0 1046 9492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088838
X-RAY DIFFRACTIONf_angle_d1.15712347
X-RAY DIFFRACTIONf_dihedral_angle_d20.0363327
X-RAY DIFFRACTIONf_chiral_restr0.0631501
X-RAY DIFFRACTIONf_plane_restr0.0061391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8499-1.87090.32361450.30893010315592
1.8709-1.89290.33631690.301532623431100
1.8929-1.9160.31991800.287332963476100
1.916-1.94030.32351770.27132403417100
1.9403-1.96580.26531680.273432933461100
1.9658-1.99270.29581730.257732973470100
1.9927-2.02120.2791700.24432393409100
2.0212-2.05140.26151650.240132693434100
2.0514-2.08340.24571560.236433143470100
2.0834-2.11760.25741710.238732573428100
2.1176-2.15410.26081910.230732813472100
2.1541-2.19320.26561710.222132483419100
2.1932-2.23540.26361780.22132333411100
2.2354-2.2810.26811690.218233093478100
2.281-2.33060.23651930.213632863479100
2.3306-2.38480.22661420.206333003442100
2.3848-2.44440.22421690.205332873456100
2.4444-2.51050.25061420.209332843426100
2.5105-2.58430.21041560.210233133469100
2.5843-2.66770.25721750.222232763451100
2.6677-2.7630.22651900.208732823472100
2.763-2.87360.20191670.217632733440100
2.8736-3.00430.25471970.216432563453100
3.0043-3.16250.25241670.21333203487100
3.1625-3.36050.24191740.20833271344599
3.3605-3.61960.20331740.181532813455100
3.6196-3.98330.19231790.169432953474100
3.9833-4.55830.15161920.159532973489100
4.5583-5.73780.18511990.174532983497100
5.7378-32.32050.17911620.19433172333493
Refinement TLS params.Method: refined / Origin x: 34.5184 Å / Origin y: -28.664 Å / Origin z: 18.3929 Å
111213212223313233
T0.1317 Å2-0.0265 Å20.0203 Å2-0.0968 Å2-0.0023 Å2--0.1205 Å2
L0.4067 °2-0.1327 °20.2036 °2-0.1526 °2-0.1579 °2--0.3076 °2
S0.0412 Å °-0.0511 Å °-0.0145 Å °0.0112 Å °0.0021 Å °0.0183 Å °0.0109 Å °-0.0239 Å °-0.0407 Å °
Refinement TLS groupSelection details: all

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