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- PDB-4ot3: Crystal structure of the S505L mutant of TAL effector dHax3 -

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Basic information

Entry
Database: PDB / ID: 4ot3
TitleCrystal structure of the S505L mutant of TAL effector dHax3
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')
  • Hax3
KeywordsDNA binding protein/DNA / DNA binding protein / DNA / DNA binding protein-DNA complex
Function / homology: / TAL effector repeat / TAL effector repeat / host cell nucleus / extracellular region / DNA / DNA (> 10) / Hax3
Function and homology information
Biological speciesXanthomonas campestris pv. armoraciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.944 Å
AuthorsDeng, D. / Wu, J.P. / Yan, C.Y. / Pan, X.J. / Yan, N.
CitationJournal: Protein Cell / Year: 2014
Title: Revisiting the TALE repeat
Authors: Deng, D. / Yan, C.Y. / Wu, J.P. / Pan, X.J. / Yan, N.
History
DepositionFeb 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 28, 2014Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hax3
B: Hax3
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)124,3876
Polymers124,3876
Non-polymers00
Water12,466692
1
A: Hax3
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)62,1933
Polymers62,1933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-67 kcal/mol
Surface area23810 Å2
MethodPISA
2
B: Hax3
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)62,1933
Polymers62,1933
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-61 kcal/mol
Surface area24680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.149, 87.383, 88.248
Angle α, β, γ (deg.)90.00, 102.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51780.586 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505L,S539G,N572H,S573D,H606N,D607G,N640H,I641D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. armoraciae (bacteria)
Gene: hax3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZD72
#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.: 692 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10%-15% PEG 3350, 12% ethanol, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.944→40 Å / Num. all: 88135 / Num. obs: 88109 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 29.18 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6T

3v6t


Resolution: 1.944→32.213 Å / FOM work R set: 0.8291 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 24.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.225 4416 5.01 %RANDOM
Rwork0.192 83693 --
obs0.1937 88109 99.78 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.478 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 130.47 Å2 / Biso mean: 35.44 Å2 / Biso min: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.6713 Å2-0 Å2-5.909 Å2
2---0.4953 Å20 Å2
3---3.4951 Å2
Refinement stepCycle: LAST / Resolution: 1.944→32.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7128 1344 0 692 9164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088851
X-RAY DIFFRACTIONf_angle_d1.25112359
X-RAY DIFFRACTIONf_chiral_restr0.071502
X-RAY DIFFRACTIONf_plane_restr0.0071400
X-RAY DIFFRACTIONf_dihedral_angle_d19.543327
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 (%)
1.9443-1.96640.30431460.28912620276695
1.9664-1.98960.34571500.284228182968100
1.9896-2.01380.32091310.270227562887100
2.0138-2.03930.2721320.258428252957100
2.0393-2.06610.32321430.254227722915100
2.0661-2.09440.26861360.243227802916100
2.0944-2.12440.28861270.244927902917100
2.1244-2.15610.27981450.226227842929100
2.1561-2.18970.24881420.222628052947100
2.1897-2.22560.2351660.211927442910100
2.2256-2.2640.26741390.213328322971100
2.264-2.30520.24581370.202527762913100
2.3052-2.34950.23061610.196827752936100
2.3495-2.39740.24241300.198328192949100
2.3974-2.44950.24981570.194127872944100
2.4495-2.50650.26651300.200827732903100
2.5065-2.56910.25591490.202328072956100
2.5691-2.63860.24941640.205527812945100
2.6386-2.71620.22621280.206428092937100
2.7162-2.80380.21341560.202427842940100
2.8038-2.9040.26451640.215927672931100
2.904-3.02010.25221720.216727802952100
3.0201-3.15750.251480.207727782926100
3.1575-3.32380.25511450.198328042949100
3.3238-3.53180.20851650.181227962961100
3.5318-3.80410.19571490.165828062955100
3.8041-4.18620.17871550.156627912946100
4.1862-4.79020.17371640.151828232987100
4.7902-6.02870.21531360.17928282964100
6.0287-32.21790.18131490.16092883303299
Refinement TLS params.Method: refined / Origin x: -3.7159 Å / Origin y: 14.3109 Å / Origin z: 24.3816 Å
111213212223313233
T0.1881 Å20.018 Å20.0134 Å2-0.1611 Å20.0017 Å2--0.1868 Å2
L0.305 °20.1124 °20.1719 °2-0.0998 °20.1275 °2--0.2945 °2
S0.0232 Å °0.0347 Å °-0.0059 Å °0.002 Å °0.0178 Å °-0.0149 Å °0.0059 Å °0.0218 Å °-0.0366 Å °
Refinement TLS groupSelection details: ALL

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