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Basic information

Entry
Database: PDB / ID: 4ldx
TitleCrystal structure of the DNA binding domain of arabidopsis thaliana auxin response factor 1 (ARF1) in complex with protomor-like sequence ER7
Components
  • Auxin response factor 1
  • ER7, forward sequence
  • ER7, reverse sequence
KeywordsTRANSCRIPTION/DNA / protein-dna complex / Transcription factor / promotor DNA / nucleus / TRANSCRIPTION-DNA complex
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
DNA / DNA (> 10) / Auxin response factor 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Auxin response factor 1
B: Auxin response factor 1
C: ER7, forward sequence
D: ER7, reverse sequence


Theoretical massNumber of molelcules
Total (without water)95,2504
Polymers95,2504
Non-polymers00
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8020 Å2
ΔGint-68 kcal/mol
Surface area37770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.520, 105.190, 127.910
Angle α, β, γ (deg.)90.00, 98.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLEULEUAA16 - 35516 - 355
21SERSERLEULEUBB16 - 35516 - 355
12DTDTDADACC1 - 211 - 21
22DTDTDADADD1 - 211 - 21

NCS ensembles :
ID
1
2

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Components

#1: Protein Auxin response factor 1


Mass: 41182.504 Da / Num. of mol.: 2 / Fragment: DNA Binding Domain, UNP residues 1-355
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: DNA chain ER7, forward sequence


Mass: 6429.158 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence resembles naturally occurring promotors and is known to bind ARF proteins
#3: DNA chain ER7, reverse sequence


Mass: 6456.200 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The sequence resembles naturally occurring promotors and is known to bind ARF proteins
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 nL complex (4 mg/mL ARF1) and 100 nL crystallization buffer (10% PEG 20K, Glycine pH 8.5, 7.5% propanediol), VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.9→35 Å / Num. obs: 25033 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 6.2
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.634 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3622 / % possible all: 98.8

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Processing

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

4ldv


Resolution: 2.9→33.81 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.868 / SU B: 38.943 / SU ML: 0.328 / Cross valid method: THROUGHOUT / ESU R Free: 0.394 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25932 1203 4.8 %RANDOM
Rwork0.21413 ---
obs0.21626 23815 98.41 %-
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: 47.427 Å2
Baniso -1Baniso -2Baniso -3
1--2.58 Å2-0 Å21.21 Å2
2--3.16 Å2-0 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.9→33.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5386 855 0 33 6274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0186488
X-RAY DIFFRACTIONr_bond_other_d0.0040.025647
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.8158971
X-RAY DIFFRACTIONr_angle_other_deg1.146313050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9695664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63322.932266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.47915939
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7831550
X-RAY DIFFRACTIONr_chiral_restr0.0760.2933
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216694
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021539
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_it2.2462.9472671
X-RAY DIFFRACTIONr_mcbond_other2.2452.9462670
X-RAY DIFFRACTIONr_mcangle_it3.9184.4063330
X-RAY DIFFRACTIONr_mcangle_other3.9174.4083331
X-RAY DIFFRACTIONr_scbond_it1.8923.3373817
X-RAY DIFFRACTIONr_scbond_other1.8923.3383818
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2714.9525642
X-RAY DIFFRACTIONr_long_range_B_refined5.94925.3627273
X-RAY DIFFRACTIONr_long_range_B_other5.94825.3687272
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A182380.14
12B182380.14
21C15320.15
22D15320.15
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 88 -
Rwork0.358 1736 -
obs--98.7 %
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)
10.5471-0.2038-0.13980.36230.0820.713-0.0824-0.09420.0025-0.04810.053-0.03630.012-0.00260.02940.1344-0.0073-0.01380.0783-0.01040.1216-9.8703-14.4222-13.5616
20.0254-0.2008-0.01952.28010.75081.2440.01470.01730.0015-0.02610.0079-0.0863-0.05380.0564-0.02270.0931-0.0239-0.00470.1081-0.02960.121-7.910218.1953-10.4256
30.36880.21660.09160.2775-0.20140.5797-0.0112-0.0526-0.0253-0.02870.0122-0.0251-0.02340.0504-0.0010.1618-0.0085-0.00610.1407-0.02010.09-13.9827-15.2128-17.4731
45.287-1.1092-0.42422.37640.70490.2492-0.1958-0.0170.1882-0.06560.22720.0320.0352-0.012-0.03130.1235-0.0665-0.04790.23970.07350.057-30.082-13.5139-12.3974
50.5736-0.10220.16411.12870.06840.7611-0.06030.1820.0129-0.00780.1334-0.04640.0133-0.0483-0.07310.095-0.01130.00090.13980.01050.0981-2.5698-17.0402-46.4192
60.16430.20590.11483.3978-0.80871.19880.02130.0101-0.1047-0.05350.2834-0.233-0.2105-0.0941-0.30470.1410.02430.11840.12270.05020.2105-3.22212.7897-53.3103
71.6782-0.0061-1.1090.66341.07432.46630.02780.0140.02330.05990.0289-0.02870.11010.0249-0.05670.1325-0.0066-0.01080.0957-0.01180.0931-0.6293-20.037-42.056
85.31381.5865-1.10370.5192-0.63552.3337-0.073-0.08050.0342-0.0115-0.0205-0.00670.00720.03810.09340.11320.01950.01450.0687-0.0420.100517.6481-16.9503-48.0943
92.59954.42820.10687.66940.08270.08790.26240.1046-0.25820.8615-0.0368-0.3231-0.20190.075-0.22560.6369-0.11620.29650.1838-0.03070.23351.433129.9948-44.8022
100.1843-0.47560.49072.70450.68623.92990.0723-0.1087-0.0522-0.6070.3965-0.0499-0.126-0.0679-0.46880.2019-0.056-0.01990.1029-0.00920.1183-17.472833.4193-16.3137
110.16070.46660.381.66231.28491.0084-0.01650.02630.0016-0.38670.109-0.1443-0.24370.0683-0.09250.39450.09130.15610.24720.05960.1821-11.786131.2356-26.2676
1217.3890.2334-7.17444.4554-0.94613.1250.4747-0.80190.70160.1127-0.3189-0.6378-0.20650.3651-0.15580.1888-0.11760.18450.2402-0.15580.35059.302931.2279-54.2934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 116
2X-RAY DIFFRACTION2A117 - 222
3X-RAY DIFFRACTION3A223 - 290
4X-RAY DIFFRACTION4A291 - 356
5X-RAY DIFFRACTION5B15 - 114
6X-RAY DIFFRACTION6B115 - 234
7X-RAY DIFFRACTION7B235 - 286
8X-RAY DIFFRACTION8B287 - 355
9X-RAY DIFFRACTION9C1 - 13
10X-RAY DIFFRACTION10C14 - 21
11X-RAY DIFFRACTION11D1 - 15
12X-RAY DIFFRACTION12D16 - 21

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