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- PDB-8oj2: Crystal structure of the DNA binding domain of M. polymorpha Auxi... -

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Basic information

Entry
Database: PDB / ID: 8oj2
TitleCrystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with protomor-like sequence IR7
Components
  • Auxin response factor
  • IR7
KeywordsTRANSCRIPTION / Molecular caliper / Auxin Response Factor / Transcription factor / DNA binding / Nucleus / Hormone Response
Function / homology
Function and homology information


auxin-activated signaling pathway / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
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 ...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
DNA / DNA (> 10) / Auxin response factor
Similarity search - Component
Biological speciesMarchantia polymorpha (liverwort)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsCrespo, I. / Weijers, D. / Boer, D.R.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2020-117028 GB-I00 Spain
Ministry of Economy and Competitiveness (MINECO)BIO2016-77883-C2-2-P Spain
Ministry of Economy and Competitiveness (MINECO)FIS2015-72574-EXP Spain
CitationJournal: To Be Published
Title: Crystal structure of the DNA binding domain of M. polymorpha Auxin Response Factor 2 (MpARF2) in complex with protomor-like sequence IR7
Authors: Crespo, I. / Weijers, D. / Boer, D.R.
History
DepositionMar 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Auxin response factor
B: IR7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3824
Polymers47,1512
Non-polymers2312
Water50428
1
A: Auxin response factor
B: IR7
hetero molecules

A: Auxin response factor
B: IR7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7638
Polymers94,3024
Non-polymers4614
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455-x-1/2,y,-z1
Buried area8470 Å2
ΔGint-76 kcal/mol
Surface area34380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.622, 79.682, 146.297
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Space group name HallI2b2c
Symmetry operation#1: x,y,z
#2: x,-y,-z+1/2
#3: -x+1/2,y,-z
#4: -x,-y+1/2,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1
#7: -x+1,y+1/2,-z+1/2
#8: -x+1/2,-y+1,z+1/2

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Components

#1: Protein Auxin response factor


Mass: 40694.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marchantia polymorpha (liverwort) / Gene: MARPO_0011s0167 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0G3FH20
#2: DNA chain IR7


Mass: 6456.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Marchantia polymorpha (liverwort)
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.65 Å3/Da / Density % sol: 53.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1 ul of protein at 4.6mg/ml in 15mM Hepes pH7.5, 150mM NaCl, 20mM DTT were mixed with 1 ul reservoir (0.2M Ammonium sulfate, 0.1M MES pH6.5, 24% PEG 3350) and equilibrated against 80 ul reservoir

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0722 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2019 / Details: KB Mirrors
RadiationMonochromator: Si(111) SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0722 Å / Relative weight: 1
ReflectionResolution: 2.558→73.148 Å / Num. obs: 12755 / % possible obs: 91.3 % / Redundancy: 12.3 % / Biso Wilson estimate: 76.71 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.123 / Rrim(I) all: 0.129 / Net I/σ(I): 12.8
Reflection shellResolution: 2.558→2.747 Å / Rmerge(I) obs: 2.67 / Num. unique obs: 638 / CC1/2: 0.448 / % possible all: 41.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBE2.3.0.1data collection
autoPROC1.0.5data processing
PHENIX1.19.2_4158phasing
Coot0.8.9.2model building
autoPROC1.0.5data reduction
autoPROC1.0.5data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→56.32 Å / SU ML: 0.4162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.1783
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.266 616 4.84 %
Rwork0.2198 12117 -
obs0.2221 12733 82.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.34 Å2
Refinement stepCycle: LAST / Resolution: 2.56→56.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 489 13 28 2792
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00352885
X-RAY DIFFRACTIONf_angle_d0.64134021
X-RAY DIFFRACTIONf_chiral_restr0.0401442
X-RAY DIFFRACTIONf_plane_restr0.0041431
X-RAY DIFFRACTIONf_dihedral_angle_d23.7767559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.820.507690.40171285X-RAY DIFFRACTION36.14
2.82-3.220.36232120.31163591X-RAY DIFFRACTION99.76
3.22-4.060.28591290.23593468X-RAY DIFFRACTION93.55
4.06-56.320.23192060.18653773X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: -17.7422207331 Å / Origin y: -0.0670656806963 Å / Origin z: -14.5942071215 Å
111213212223313233
T0.384215452718 Å2-0.0599458576355 Å20.0104082653289 Å2-0.39963268881 Å20.0216679925427 Å2--0.381634283462 Å2
L0.475566485216 °2-0.436153125866 °2-0.141054869444 °2-0.406102735712 °20.0143636332676 °2--1.67007306755 °2
S0.0399468229809 Å °0.0850907582895 Å °-0.0340344840407 Å °0.0188931028434 Å °-0.000524023577062 Å °0.26614297162 Å °0.466792267288 Å °-0.0700369595245 Å °-0.00395093591562 Å °
Refinement TLS groupSelection details: all

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