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- PDB-3v6p: Crystal structure of the DNA-binding domain of dHax3, a TAL effector -

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Basic information

Entry
Database: PDB / ID: 3v6p
TitleCrystal structure of the DNA-binding domain of dHax3, a TAL effector
ComponentsdHax3
KeywordsDNA BINDING PROTEIN / 11 tandem repeats / Sequence specific DNA recognition protein
Biological speciesXanthomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.401 Å
AuthorsDeng, D. / Yan, C.Y. / Pan, X.J. / Wang, J.W. / Shi, Y.G. / Yan, N.
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 1.1Mar 20, 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

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Assembly

Deposited unit
A: dHax3


Theoretical massNumber of molelcules
Total (without water)45,8851
Polymers45,8851
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.762, 95.507, 153.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein dHax3


Mass: 45884.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas (bacteria) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 8-12% PEG 3350(w/v), 0.1M sodium citrate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.97915
SYNCHROTRONSSRF BL17U21.25501, 1.22959, 1.28105
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDSep 15, 2011
ADSC QUANTUM 315r2CCDJun 25, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELSINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979151
21.255011
31.229591
41.281051
ReflectionResolution: 2.4→40 Å / Num. all: 21790 / Num. obs: 20832 / % possible obs: 95.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 53.42 Å2
Reflection shellResolution: 2.4→2.49 Å / % possible all: 98.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
RESOLVEmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.401→29.435 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.7586 / SU ML: 0.75 / σ(F): 1.34 / Phase error: 29.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 1043 5.01 %RANDOM
Rwork0.2111 ---
all0.2137 21790 --
obs0.2137 20816 95.51 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.42 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 146.87 Å2 / Biso mean: 63.8633 Å2 / Biso min: 32.07 Å2
Baniso -1Baniso -2Baniso -3
1--8.7565 Å20 Å2-0 Å2
2--20.2424 Å20 Å2
3----10.8384 Å2
Refinement stepCycle: LAST / Resolution: 2.401→29.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 0 49 2749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092748
X-RAY DIFFRACTIONf_angle_d1.2343752
X-RAY DIFFRACTIONf_dihedral_angle_d19.5361010
X-RAY DIFFRACTIONf_chiral_restr0.078468
X-RAY DIFFRACTIONf_plane_restr0.005499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4014-2.5280.38921400.30712835297597
2.528-2.68630.37921550.2752829298498
2.6863-2.89350.30011520.27142882303498
2.8935-3.18440.31381660.25492825299197
3.1844-3.64450.27261460.23952837298397
3.6445-4.58880.22381510.18042796294794
4.5888-29.43730.21821330.172769290289
Refinement TLS params.Method: refined / Origin x: -26.9012 Å / Origin y: 13.1417 Å / Origin z: 22.005 Å
111213212223313233
T0.4021 Å20.007 Å2-0.0047 Å2-0.4152 Å20.022 Å2--0.3883 Å2
L0.1558 °20.1355 °2-0.0493 °2-0.2432 °2-0.0987 °2--0.2063 °2
S0.0255 Å °-0.0399 Å °-0.0349 Å °0.0291 Å °-0.0064 Å °0.0019 Å °0.0318 Å °0.0088 Å °-0.0219 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA303 - 675
2X-RAY DIFFRACTION1allA1 - 49

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