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- PDB-4osw: Crystal structure of the S505E mutant of TAL effector dHax3 -

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Basic information

Entry
Database: PDB / ID: 4osw
TitleCrystal structure of the S505E 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: 2.302 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4678
Polymers124,4196
Non-polymers492
Water5,747319
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')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2585
Polymers62,2093
Non-polymers492
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-70 kcal/mol
Surface area23940 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)62,2093
Polymers62,2093
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-59 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.949, 87.647, 87.437
Angle α, β, γ (deg.)90.00, 102.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51796.543 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505E,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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.46 Å3/Da / Density % sol: 50.07 %
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

DiffractionMean temperature: 100 K
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: 2.3→40 Å / Num. all: 53536 / Num. obs: 53514 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 39.29 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: 2.302→30.864 Å / FOM work R set: 0.7935 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 2717 5.08 %
Rwork0.1976 50797 -
obs0.2 53514 99.83 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.444 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso max: 150.91 Å2 / Biso mean: 46.69 Å2 / Biso min: 20.06 Å2
Baniso -1Baniso -2Baniso -3
1--1.4847 Å2-0 Å2-4.4136 Å2
2--0.0444 Å20 Å2
3---4.7787 Å2
Refinement stepCycle: LAST / Resolution: 2.302→30.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7071 1381 2 319 8773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098836
X-RAY DIFFRACTIONf_angle_d1.55112346
X-RAY DIFFRACTIONf_chiral_restr0.081500
X-RAY DIFFRACTIONf_plane_restr0.0111393
X-RAY DIFFRACTIONf_dihedral_angle_d20.1123324
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3021-2.3440.32571270.27022602272998
2.344-2.3890.32421450.262726402785100
2.389-2.43780.35061430.25426812824100
2.4378-2.49070.30211320.252126742806100
2.4907-2.54870.30641370.248726662803100
2.5487-2.61240.32081450.242426402785100
2.6124-2.6830.28561280.248826802808100
2.683-2.76190.25611460.22826812827100
2.7619-2.85090.30961340.238826682802100
2.8509-2.95280.30921270.24826902817100
2.9528-3.07090.33661480.238126662814100
3.0709-3.21050.251550.218326602815100
3.2105-3.37960.25971350.22127082843100
3.3796-3.5910.25171560.195826502806100
3.591-3.86780.23481480.18326942842100
3.8678-4.25610.19961460.158426712817100
4.2561-4.86990.18721490.151727012850100
4.8699-6.12770.22521700.18226712841100
6.1277-30.86660.18641460.15522754290099
Refinement TLS params.Method: refined / Origin x: -3.6522 Å / Origin y: 13.946 Å / Origin z: 24.0705 Å
111213212223313233
T0.2449 Å20.0182 Å20.0176 Å2-0.2338 Å20.0015 Å2--0.2462 Å2
L0.2517 °20.1097 °20.1689 °2-0.2432 °20.1509 °2--0.3233 °2
S0.014 Å °0.0206 Å °0.0018 Å °-0.0263 Å °0.0089 Å °0.0285 Å °-0.0397 Å °-0.007 Å °-0.0227 Å °
Refinement TLS groupSelection details: ALL

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