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- PDB-4ost: Crystal structure of the S505C mutant of TAL effector dHax3 -

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Basic information

Entry
Database: PDB / ID: 4ost
TitleCrystal structure of the S505C 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: 1.996 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

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')


Theoretical massNumber of molelcules
Total (without water)124,3676
Polymers124,3676
Non-polymers00
Water9,476526
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)62,1833
Polymers62,1833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-63 kcal/mol
Surface area24010 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)62,1833
Polymers62,1833
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-61 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.120, 87.018, 87.906
Angle α, β, γ (deg.)90.00, 102.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51770.570 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505C,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.: 526 / 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: 2.43 Å3/Da / Density % sol: 49.44 %
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: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.996→40 Å / Num. all: 80661 / Num. obs: 80636 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 27.92 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: 1.996→39.383 Å / FOM work R set: 0.8353 / SU ML: 0.22 / σ(F): 1.35 / Phase error: 23.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.233 4035 5 %
Rwork0.2013 76601 -
obs0.2029 80636 99.53 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.02 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 108.44 Å2 / Biso mean: 33.63 Å2 / Biso min: 14.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.4628 Å2-0 Å2-6.0989 Å2
2---1.035 Å20 Å2
3---4.5043 Å2
Refinement stepCycle: LAST / Resolution: 1.996→39.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7089 1344 0 526 8959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078821
X-RAY DIFFRACTIONf_angle_d1.2112316
X-RAY DIFFRACTIONf_chiral_restr0.0681497
X-RAY DIFFRACTIONf_plane_restr0.0061394
X-RAY DIFFRACTIONf_dihedral_angle_d19.5973316
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9963-2.01980.29171340.28062477261194
2.0198-2.04450.25921350.25422629276499
2.0445-2.07030.29261250.25852634275999
2.0703-2.09760.28321300.251826362766100
2.0976-2.12630.29011460.25012614276099
2.1263-2.15670.27251410.245226332774100
2.1567-2.18890.29281430.233226332776100
2.1889-2.22310.24311620.226925772739100
2.2231-2.25950.25551180.218926972815100
2.2595-2.29850.21821360.211626172753100
2.2985-2.34030.22791380.215426452783100
2.3403-2.38530.24361400.215926532793100
2.3853-2.43390.30371580.213126412799100
2.4339-2.48690.26931490.20926182767100
2.4869-2.54470.23151390.21426322771100
2.5447-2.60830.24241340.212526462780100
2.6083-2.67880.25831210.228726582779100
2.6788-2.75760.24951130.211926912804100
2.7576-2.84660.27681320.221826582790100
2.8466-2.94830.29541370.229526462783100
2.9483-3.06630.24121270.22826602787100
3.0663-3.20580.25031350.216626662801100
3.2058-3.37480.26741370.208826652802100
3.3748-3.58610.22851620.18692613277599
3.5861-3.86270.18131550.17612642279799
3.8627-4.25110.19721450.167126512796100
4.2511-4.86520.20241640.163426492813100
4.8652-6.1260.23131450.18826802825100
6.126-39.39090.17711340.16512740287499
Refinement TLS params.Method: refined / Origin x: -34.4473 Å / Origin y: 14.6344 Å / Origin z: -18.4028 Å
111213212223313233
T0.18 Å20.0191 Å20.0158 Å2-0.1541 Å2-0.0026 Å2--0.1756 Å2
L0.3286 °20.1039 °20.1996 °2-0.125 °20.1232 °2--0.3 °2
S0.0329 Å °0.0277 Å °-0.0072 Å °0.0043 Å °0.0171 Å °-0.0128 Å °-0.0002 Å °0.0015 Å °-0.0474 Å °
Refinement TLS groupSelection details: ALL

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