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- PDB-4osl: Crystal structure of TAL effector reveals the recognition between... -

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Basic information

Entry
Database: PDB / ID: 4osl
TitleCrystal structure of TAL effector reveals the recognition between histidine and guanine
Components
  • DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*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: 2.447 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*GP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4878
Polymers124,4396
Non-polymers492
Water7,260403
1
A: Hax3
I: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*TP*CP*TP*CP*TP*CP*T)-3')
J: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2444
Polymers62,2193
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-70 kcal/mol
Surface area23960 Å2
MethodPISA
2
B: Hax3
G: DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*GP*TP*CP*TP*CP*TP*CP*T)-3')
H: DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2444
Polymers62,2193
Non-polymers241
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-66 kcal/mol
Surface area24630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.530, 87.609, 87.843
Angle α, β, γ (deg.)90.00, 102.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Hax3


Mass: 51805.574 Da / Num. of mol.: 2 / Fragment: UNP residues 231-720
Mutation: N300H,I301D,N368H,I369D,H402N,D403G,H436N,D437G,H470N,D471G,S505H,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*GP*TP*CP*TP*CP*TP*CP*T)-3')


Mass: 5086.280 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain DNA (5'-D(*AP*GP*AP*GP*AP*GP*AP*CP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3')


Mass: 5327.502 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.: 403 / 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: 49.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10%-15% PEG3350, 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: 1.5418 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.447→40 Å / Num. all: 42926 / Num. obs: 42796 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 35.22 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V6T

3v6t


Resolution: 2.447→26.546 Å / FOM work R set: 0.8108 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 25.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 2163 5.05 %RANDOM
Rwork0.2248 40633 --
all0.2257 42926 --
obs0.2257 42796 95.94 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.115 Å2 / ksol: 0.342 e/Å3
Displacement parametersBiso max: 115.24 Å2 / Biso mean: 37.44 Å2 / Biso min: 11.17 Å2
Baniso -1Baniso -2Baniso -3
1-3.4039 Å20 Å2-3.327 Å2
2---2.8944 Å2-0 Å2
3---0.9334 Å2
Refinement stepCycle: LAST / Resolution: 2.447→26.546 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7100 1381 2 403 8886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088813
X-RAY DIFFRACTIONf_angle_d1.69312302
X-RAY DIFFRACTIONf_chiral_restr0.0751495
X-RAY DIFFRACTIONf_plane_restr0.0121386
X-RAY DIFFRACTIONf_dihedral_angle_d20.8723317
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4471-2.5040.29471410.30612553269492
2.504-2.56650.38941400.32352637277794
2.5665-2.63590.37021500.3442667281795
2.6359-2.71330.38161140.33662693280795
2.7133-2.80080.37191410.3362663280495
2.8008-2.90080.38611390.34852663280295
2.9008-3.01680.32751480.29752708285696
3.0168-3.15390.29141260.25952732285896
3.1539-3.31990.2411310.24762702283396
3.3199-3.52740.21481550.21892753290897
3.5274-3.79910.2011610.19672718287998
3.7991-4.18010.21781540.17522757291197
4.1801-4.78190.1861660.16492744291097
4.7819-6.01310.20861320.18512802293498
6.0131-26.54770.17981650.16012841300698
Refinement TLS params.Method: refined / Origin x: -3.7274 Å / Origin y: 14.0705 Å / Origin z: 24.1741 Å
111213212223313233
T0.1181 Å20.036 Å20.0149 Å2-0.0745 Å20.0102 Å2--0.0993 Å2
L0.3223 °20.1758 °20.1373 °2-0.2084 °20.1971 °2--0.2717 °2
S0.0396 Å °-0.0032 Å °0.0056 Å °-0.01 Å °0.0036 Å °0.025 Å °-0.0469 Å °-0.0045 Å °-0.0414 Å °
Refinement TLS groupSelection details: ALL

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