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- PDB-4ldy: Crystal structure of the DNA binding domain of the G245A mutant o... -

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Basic information

Entry
Database: PDB / ID: 4ldy
TitleCrystal structure of the DNA binding domain of the G245A mutant of arabidopsis thaliana auxin reponse factor 1
ComponentsAuxin response factor 1
KeywordsTRANSCRIPTION / Transcription factor / DNA binding / nucleus
Function / homology
Function and homology information


leaf senescence / cell death / response to auxin / auxin-activated signaling pathway / sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
SH3 type barrels. - #1040 / Auxin response factor domain / Auxin response factor / Auxin response factor ancillary domain / DNA-binding pseudobarrel domain / At1g16640 B3 domain / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain ...SH3 type barrels. - #1040 / Auxin response factor domain / Auxin response factor / Auxin response factor ancillary domain / DNA-binding pseudobarrel domain / At1g16640 B3 domain / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain / DNA-binding pseudobarrel domain superfamily / : / PB1 domain profile. / SH3 type barrels. / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Auxin response factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBoer, D.R. / Freire-Rios, A. / van den Berg, W.M.A. / Weijers, D. / Coll, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Structural Basis for DNA Binding Specificity by the Auxin-Dependent ARF Transcription Factors.
Authors: Boer, D.R. / Freire-Rios, A. / van den Berg, W.A. / Saaki, T. / Manfield, I.W. / Kepinski, S. / Lopez-Vidrieo, I. / Franco-Zorrilla, J.M. / de Vries, S.C. / Solano, R. / Weijers, D. / Coll, M.
History
DepositionJun 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / 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 / _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: Auxin response factor 1
B: Auxin response factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2584
Polymers82,1872
Non-polymers712
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-29 kcal/mol
Surface area33320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 84.240, 78.960
Angle α, β, γ (deg.)90.00, 114.76, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Auxin response factor 1


Mass: 41093.391 Da / Num. of mol.: 2 / Fragment: DNA Binding Domain, UNP residues 1-355 / Mutation: G245A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARF1, At1g59750, F23H11.7 / Plasmid: pTWIN1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: Q8L7G0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.75 l of 13 mg/ml Arf1dbd-g245a +0.75 l crystallization buffer (100 mM bis-tris-propane pH 7.0, 0.7 M succinic acid), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→71.7 Å / Num. obs: 38764 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.8 / Num. unique all: 5641 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LDV

4ldv


Resolution: 2.3→63.91 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 16.446 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2588 1943 5 %RANDOM
Rwork0.21015 ---
obs0.21263 36804 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.556 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å21.33 Å2
2---0.58 Å2-0 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 2.3→63.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5239 0 2 109 5350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195387
X-RAY DIFFRACTIONr_bond_other_d0.0010.025037
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.9427302
X-RAY DIFFRACTIONr_angle_other_deg0.799311608
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5325645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14822.797261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28915912
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6951551
X-RAY DIFFRACTIONr_chiral_restr0.090.2785
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216016
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021295
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.36832595
X-RAY DIFFRACTIONr_mcbond_other2.3682.9982594
X-RAY DIFFRACTIONr_mcangle_it3.834.4823232
X-RAY DIFFRACTIONr_mcangle_other3.834.4833233
X-RAY DIFFRACTIONr_scbond_it2.6043.2862792
X-RAY DIFFRACTIONr_scbond_other2.6043.2872793
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2154.814070
X-RAY DIFFRACTIONr_long_range_B_refined7.11524.2115977
X-RAY DIFFRACTIONr_long_range_B_other7.10424.1855969
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 129 -
Rwork0.308 2750 -
obs--99.97 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.73420.3063-5.24410.4452-0.16497.5603-0.18690.0977-0.2167-0.1787-0.0325-0.1360.1312-0.08280.21940.1634-0.02490.02410.21080.00610.1643-4.493-21.3025-45.8045
27.93120.2631-0.315212.07863.42755.61830.0654-0.04470.11460.07080.0225-0.167-0.08670.2507-0.0880.2343-0.0370.01760.0956-0.05640.2479-15.372-40.4088-41.76
310.00410.2773-1.83430.012-0.05520.3420.0239-0.1017-0.13920.0026-0.02950.0125-0.02010.04030.00570.1385-0.0149-0.01260.1255-0.00530.194816.1506-19.3744-9.5661
48.9981.25630.3816.5410.97875.1147-0.1627-0.0750.9127-0.03710.09240.126-0.29550.21770.07030.3368-0.0388-0.09330.0881-0.06230.66489.1107-0.3422-2.5164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 288
2X-RAY DIFFRACTION2A289 - 356
3X-RAY DIFFRACTION3B16 - 288
4X-RAY DIFFRACTION4B289 - 356

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