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- PDB-6l5k: ARF5 Aux/IAA17 Complex -

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Basic information

Entry
Database: PDB / ID: 6l5k
TitleARF5 Aux/IAA17 Complex
Components
  • Auxin response factor 5
  • Auxin-responsive protein IAA17
KeywordsTRANSCRIPTION / auxin / auxin response factor / AUX/IAA / Complex
Function / homology
Function and homology information


meristem development / longitudinal axis specification / positive regulation of leaf senescence / xylem and phloem pattern formation / leaf vascular tissue pattern formation / root development / flower development / response to auxin / auxin-activated signaling pathway / embryo development ending in seed dormancy ...meristem development / longitudinal axis specification / positive regulation of leaf senescence / xylem and phloem pattern formation / leaf vascular tissue pattern formation / root development / flower development / response to auxin / auxin-activated signaling pathway / embryo development ending in seed dormancy / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / identical protein binding / nucleus
Similarity search - Function
AUX/IAA protein / Auxin response factor domain / Auxin response factor / Auxin response factor / AUX/IAA domain / AUX/IAA family / B3 DNA binding domain / B3 DNA binding domain / B3 DNA-binding domain profile. / B3 DNA binding domain ...AUX/IAA protein / Auxin response factor domain / Auxin response factor / Auxin response factor / 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
Similarity search - Domain/homology
Auxin response factor 5 / Auxin-responsive protein IAA17
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsRyu, K.S. / Suh, J.Y. / Cha, S.Y. / Kim, Y.I. / Park, C.K.
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Determinants of PB1 Domain Interactions in Auxin Response Factor ARF5 and Repressor IAA17.
Authors: Kim, Y. / Park, C. / Cha, S. / Han, M. / Ryu, K.S. / Suh, J.Y.
History
DepositionOct 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Auxin response factor 5
B: Auxin-responsive protein IAA17


Theoretical massNumber of molelcules
Total (without water)23,7412
Polymers23,7412
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-4 kcal/mol
Surface area9930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.894, 79.894, 116.025
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Auxin response factor 5 / Auxin-responsive protein IAA24 / Transcription factor MONOPTEROS


Mass: 10971.138 Da / Num. of mol.: 1 / Mutation: A788G,K797D,C825S,C866S,C869S,D183N,D187N,C203A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ARF5, IAA24, MP, At1g19850, F6F9.10 / Production host: Escherichia coli (E. coli) / References: UniProt: P93024
#2: Protein Auxin-responsive protein IAA17 / Auxin response 3 / Indoleacetic acid-induced protein 17


Mass: 12769.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: IAA17, AXR3, At1g04250, F19P19.31 / Production host: Escherichia coli (E. coli) / References: UniProt: P93830
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 8.5 / Details: Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 8612 / % possible obs: 97.99 % / Redundancy: 8.9 % / Biso Wilson estimate: 66.36 Å2 / CC1/2: 0.989 / Net I/σ(I): 43.2
Reflection shellResolution: 2.9→3.01 Å / Redundancy: 4 % / Num. unique obs: 8594 / CC1/2: 0.438

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data collection
HKL-2000data scaling
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4chk,2muk

4chk

2muk


Resolution: 2.91→35.73 Å / SU ML: 0.5638 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 31.2326
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2698 860 10 %
Rwork0.2257 7736 -
obs0.2302 8596 98.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 81.02 Å2
Refinement stepCycle: LAST / Resolution: 2.91→35.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1381 0 0 15 1396
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01061412
X-RAY DIFFRACTIONf_angle_d1.15791908
X-RAY DIFFRACTIONf_chiral_restr0.0596206
X-RAY DIFFRACTIONf_plane_restr0.0061240
X-RAY DIFFRACTIONf_dihedral_angle_d7.443839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-3.090.41341360.37521225X-RAY DIFFRACTION95.58
3.09-3.330.33721400.31981256X-RAY DIFFRACTION97.42
3.33-3.660.32311400.25651265X-RAY DIFFRACTION98.8
3.66-4.190.26541420.19741276X-RAY DIFFRACTION98.34
4.19-5.280.21361450.17171305X-RAY DIFFRACTION98.77
5.28-35.730.24011570.20611409X-RAY DIFFRACTION99.43
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)
18.78094786882-0.5342046830722.063945731574.63001586971-1.492454856164.266812335450.115892814369-1.178153164780.1666074938350.6122367379311.540335246941.778249740040.0624558493516-2.607788506180.5921301744371.60180255362-0.0221454567638-0.2277607259240.866682628901-0.1606573464610.669987199664-18.7358452676-12.7344700375-19.4244655915
28.149601813371.638216047342.950814093651.550569782241.563298751547.952489493590.997518826816-1.01959087733-1.69032296186-0.431601686170.170043396919-0.3605519050251.54071537098-0.189128628151-0.154036808621.162359944990.302800283806-0.3265356569750.657165439634-0.1446151480130.477253970587-10.4269033153-9.46141839731-21.2149014707
32.273247225421.524736039941.066195372563.146736887273.483899644784.68490823076-0.77844719459-1.58828403955-1.538923597552.139762272221.38654660038-0.577220757788-0.3106491707940.215507198822-0.267979796961.22506430871-0.0850777196189-0.2874123730840.786924064050.1410882011260.456633946546-4.34150264251.60229781839-25.7928103962
44.47624170270.02050848167880.2100759924189.51048072884-1.206246921873.67516423640.207741437535-0.8337641519490.0158925925310.6299362653830.09927465263580.4396165767030.55196786838-0.186732205738-0.4951488050990.7081944635180.0123203540929-0.1295615338130.677494649321-0.05291630288610.361504901661-17.74363777880.4800582418-17.383855649
54.15251103264-1.422907153590.1957821956426.073049234741.947816454378.190149017280.456355845629-0.05275706965810.284022814094-0.526699049586-0.456779577466-0.629606018911-0.2005644848441.6876856956-0.2411436032120.972459673699-0.108990494902-0.0007628229228330.981276632525-0.1348394530170.33643554137-13.178034506212.5200638588-8.23521694897
65.419862145451.59710548907-5.233566005131.6782739536-1.335379203015.31521901631-1.186387400823.22695008794-0.386938573335-0.378070123793-1.44188222545-1.426096252550.05884178863591.29640731172-1.600803563150.6514627627280.01646767041190.9047822806510.6409199327630.7864193001921.24931924385-14.80713111723.5345546488-15.6727607158
76.56447110282-1.80484386994-1.323074063338.051779198950.7917764927442.20448590203-0.193599440478-1.043703847960.1090734275541.193062758250.3601558756370.654358416586-0.00225248098889-0.6933039106040.2914017798960.8464600841580.1025199827950.06808785199731.14667533689-0.3008985058520.523698475811-22.470112844115.2565417143-0.743797717395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 792 through 800 )
2X-RAY DIFFRACTION2chain 'A' and (resid 801 through 827 )
3X-RAY DIFFRACTION3chain 'A' and (resid 828 through 841 )
4X-RAY DIFFRACTION4chain 'A' and (resid 842 through 883 )
5X-RAY DIFFRACTION5chain 'B' and (resid 109 through 149 )
6X-RAY DIFFRACTION6chain 'B' and (resid 150 through 177 )
7X-RAY DIFFRACTION7chain 'B' and (resid 178 through 211 )

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