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- PDB-4ldv: Crystal structure of the DNA binding domain of A. thailana auxin ... -

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Basic information

Entry
Database: PDB / ID: 4ldv
TitleCrystal structure of the DNA binding domain of A. thailana auxin response factor 1
ComponentsAuxin response factor 1
KeywordsTRANSCRIPTION / Transcription Factor / DNA binding / Nucleus
Function / homology
Function and homology information


leaf senescence / response to auxin / cell death / 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 / 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 / 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. / PB1 domain / SH3 type barrels. / Roll / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / IODIDE ION / Auxin response factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.2Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxin response factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,68514
Polymers41,0791
Non-polymers60513
Water5,368298
1
A: Auxin response factor 1
hetero molecules

A: Auxin response factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,36928
Polymers82,1592
Non-polymers1,21026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6720 Å2
ΔGint-158 kcal/mol
Surface area32470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.362, 126.256, 83.672
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Auxin response factor 1


Mass: 41079.363 Da / Num. of mol.: 1 / Fragment: DNA Binding Domain
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-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.75 l of 4mg/mL ARF1DBD + 0.75 l crystallization buffer (2.9 M NaFormate, 0.1 M MES 6.0, 50 mM KI), pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.45→39.08 Å / Num. obs: 81768 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 7.3
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.4 / Num. unique all: 11957 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet derivative

Resolution: 1.45→39.08 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.405 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24344 4079 5 %RANDOM
Rwork0.2093 ---
obs0.21101 77670 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å2-0 Å2
2---0.61 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2591 0 23 298 2912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192857
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.943881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0545360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29922.734139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35415502
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2441528
X-RAY DIFFRACTIONr_chiral_restr0.110.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212196
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.4131.5271361
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3942.271706
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7161.7511495
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined6.95413.8344404
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.448→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 279 -
Rwork0.376 5486 -
obs--94.73 %
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)
12.31610.3002-0.64342.3105-0.2251.74140.0028-0.09470.2776-0.0230.0616-0.2726-0.26450.2058-0.06440.0455-0.03230.00460.0281-0.02220.075216.580736.2228-20.8238
22.11271.85260.83273.89731.01162.2680.0518-0.0471-0.27550.1443-0.06920.25230.4475-0.37520.01740.1248-0.07020.0260.0697-0.01280.145825.723467.0912-20.5392
32.67830.86922.75180.28660.89793.0797-0.0651-0.13660.1007-0.0061-0.03360.0228-0.15840.03770.09880.1022-0.0395-0.03840.1386-0.02120.025318.36635.8256-8.7095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 115
2X-RAY DIFFRACTION2A120 - 226
3X-RAY DIFFRACTION3A233 - 356

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