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- PDB-6wig: Structure of STENOFOLIA Protein HD domain bound with DNA -

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Basic information

Entry
Database: PDB / ID: 6wig
TitleStructure of STENOFOLIA Protein HD domain bound with DNA
Components
  • DNA (5'-D(P*CP*TP*TP*GP*AP*AP*TP*AP*AP*AP*TP*CP*AP*TP*TP*AP*AP*TP*TP*TP*GP*C)-3')
  • DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*AP*AP*TP*GP*AP*TP*TP*TP*AP*TP*TP*CP*AP*AP*G)-3')
  • STENOFOLIA
KeywordsPLANT PROTEIN/DNA / STF / HD domain / WOX / transcriptional factor / PLANT PROTEIN / PLANT PROTEIN-DNA complex
Function / homology
Function and homology information


plant organ development / DNA-binding transcription factor activity / DNA binding / nucleus
Similarity search - Function
Protein WUSCHEL-like / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / STENOFOLIA
Similarity search - Component
Biological speciesMedicago truncatula (barrel medic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsDeng, J. / Peng, S. / Pathak, P.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structure of the unique tetrameric STENOFOLIA homeodomain bound with target promoter DNA.
Authors: Pathak, P.K. / Zhang, F. / Peng, S. / Niu, L. / Chaturvedi, J. / Elliott, J. / Xiang, Y. / Tadege, M. / Deng, J.
History
DepositionApr 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: STENOFOLIA
B: STENOFOLIA
C: DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*AP*AP*TP*GP*AP*TP*TP*TP*AP*TP*TP*CP*AP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*TP*GP*AP*AP*TP*AP*AP*AP*TP*CP*AP*TP*TP*AP*AP*TP*TP*TP*GP*C)-3')


Theoretical massNumber of molelcules
Total (without water)38,2344
Polymers38,2344
Non-polymers00
Water79344
1
B: STENOFOLIA
C: DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*AP*AP*TP*GP*AP*TP*TP*TP*AP*TP*TP*CP*AP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*TP*GP*AP*AP*TP*AP*AP*AP*TP*CP*AP*TP*TP*AP*AP*TP*TP*TP*GP*C)-3')

A: STENOFOLIA


Theoretical massNumber of molelcules
Total (without water)38,2344
Polymers38,2344
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_846-x+3,y-1/2,-z+11
Buried area5670 Å2
ΔGint-34 kcal/mol
Surface area17150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.061, 49.489, 69.810
Angle α, β, γ (deg.)90.000, 106.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein STENOFOLIA


Mass: 12367.872 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Medicago truncatula (barrel medic) / Gene: STF / Production host: Escherichia coli (E. coli) / References: UniProt: G0ZGT3
#2: DNA chain DNA (5'-D(P*GP*CP*AP*AP*AP*TP*TP*AP*AP*TP*GP*AP*TP*TP*TP*AP*TP*TP*CP*AP*AP*G)-3')


Mass: 6773.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Medicago truncatula (barrel medic)
#3: DNA chain DNA (5'-D(P*CP*TP*TP*GP*AP*AP*TP*AP*AP*AP*TP*CP*AP*TP*TP*AP*AP*TP*TP*TP*GP*C)-3')


Mass: 6724.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Medicago truncatula (barrel medic)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.08 Å3/Da / Density % sol: 40.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: .15 M sodium chloride 28 % v/v PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Aug 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 17541 / % possible obs: 95.2 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 4.4
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.662 / Num. unique obs: 1431 / CC1/2: 0.814 / % possible all: 77.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.06
RfactorNum. reflection% reflection
Rfree0.2498 1731 9.9 %
Rwork0.1943 --
obs0.1997 17488 94.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.87 Å2 / Biso mean: 59.9257 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 902 0 44 2231
Biso mean---46.51 -
Num. residues----194
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012322
X-RAY DIFFRACTIONf_angle_d1.2143313
X-RAY DIFFRACTIONf_chiral_restr0.066353
X-RAY DIFFRACTIONf_plane_restr0.007277
X-RAY DIFFRACTIONf_dihedral_angle_d29.8791246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.105-2.16680.41471040.3077106276
2.1668-2.23670.35071380.3031115885
2.2367-2.31670.33931390.2803126692
2.3167-2.40940.32131450.2668131295
2.4094-2.51910.31471490.2433134698
2.5191-2.65190.29291490.24641381100
2.6519-2.8180.26921580.2404135699
2.818-3.03550.2891570.2379135898
3.0355-3.34090.28681340.2211134697
3.3409-3.82420.25071540.1693138098
3.8242-4.81730.22291480.1539136799
4.8173-46.10.18571560.1587142599
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)
16.12510.31375.24570.13690.28984.9810.12390.1347-0.6414-0.18920.57960.32810.7440.5226-0.5260.540.0724-0.09430.7099-0.03060.530683.53538.70538.1273
28.4938-3.19192.04424.5155-3.27557.2306-0.202-0.3981.71590.850.1765-0.3364-0.81940.10920.13920.5087-0.11630.02770.3427-0.0770.594475.99355.545733.3328
37.74771.64991.33933.72981.41235.3312-0.1251.36180.5464-0.77480.2801-0.4553-0.70030.7029-0.00910.4546-0.14440.00240.4620.08660.478978.447752.204222.9925
45.84930.8294-6.07480.2678-1.12576.7848-1.0899-0.45160.4070.1528-0.7696-0.5183-0.1611-0.3426-0.05590.382-0.1426-0.23560.66390.0820.755884.803246.259230.8592
59.3849-3.1583-4.75266.21471.58793.84950.174-0.61230.01570.40140.03850.3499-0.4932-0.0067-0.15890.4126-0.0208-0.01530.3770.00690.304364.51747.855331.9255
69.2796-2.8565-2.74892.66032.67032.78270.68940.7117-0.0861-0.5169-0.04940.43550.1566-0.1787-1.02381.09470.1876-0.06750.8120.05950.760949.07161.608547.873
78.99171.38990.38594.8389-0.89547.8597-0.18670.6945-0.1612-1.63270.58990.97030.7725-0.2911-0.0650.6811-0.03430.0180.5075-0.11890.45566.930228.42852.995
86.424-0.5257-0.57316.5935-0.37412.53460.0563-0.574-0.55740.06940.4034-1.44370.87480.6561-0.19920.51710.00660.04470.5123-0.06660.81575.004325.630512.2211
91.8858-1.0081.34672.5368-2.59742.7198-0.64390.90540.3845-1.2725-0.2571-0.9602-0.08140.9462-0.22190.9876-0.0630.2150.8183-0.2440.695775.24531.11961.3769
104.24544.7065-3.59085.1824-4.13017.6827-0.2399-0.53240.5583-0.42340.28550.57860.3967-0.0009-0.18060.47460.034-0.05410.3532-0.02730.383160.191728.225414.4974
119.1286-3.19626.25063.9641-3.52444.9158-0.2162-0.0758-0.47520.64150.3379-0.2334-0.9335-0.1814-0.2930.6378-0.0028-0.13080.4441-0.01390.432849.844538.9691-6.2986
121.4922-0.67882.26853.2341-1.42739.4757-0.18310.14940.05060.17470.23930.0568-0.69370.1153-0.06480.2656-0.04360.00850.3209-0.02380.377264.7437.957527.0028
137.7209-2.51634.1623.29330.81344.2208-0.2823-0.29250.17170.3489-0.34640.0512-0.7431-0.10890.71940.2995-0.0246-0.01910.3545-0.01370.381169.256941.150838.3835
145.87741.22552.21465.96060.68642.57740.46110.0273-0.0215-0.61960.35480.6613-0.17980.0873-0.69580.51050.02-0.09070.43490.02550.415859.786438.749315.9533
156.03381.96021.47394.4160.99996.06170.0291-0.2012-0.73630.30620.2713-0.13250.4530.1476-0.17030.57310.0365-0.1060.4279-0.05230.435746.798637.2723-8.8384
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 89 through 100 )A89 - 100
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 112 )A101 - 112
3X-RAY DIFFRACTION3chain 'A' and (resid 113 through 132 )A113 - 132
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 137 )A133 - 137
5X-RAY DIFFRACTION5chain 'A' and (resid 138 through 161 )A138 - 161
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 172 )A162 - 172
7X-RAY DIFFRACTION7chain 'B' and (resid 92 through 112 )B92 - 112
8X-RAY DIFFRACTION8chain 'B' and (resid 113 through 131 )B113 - 131
9X-RAY DIFFRACTION9chain 'B' and (resid 132 through 137 )B132 - 137
10X-RAY DIFFRACTION10chain 'B' and (resid 138 through 159 )B138 - 159
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 10 )C1 - 10
12X-RAY DIFFRACTION12chain 'C' and (resid 11 through 22 )C11 - 22
13X-RAY DIFFRACTION13chain 'D' and (resid 1 through 5 )D1 - 5
14X-RAY DIFFRACTION14chain 'D' and (resid 6 through 15 )D6 - 15
15X-RAY DIFFRACTION15chain 'D' and (resid 16 through 22 )D16 - 22

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