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- PDB-4qtr: Computational design of co-assembling protein-DNA nanowires -

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Basic information

Entry
Database: PDB / ID: 4qtr
TitleComputational design of co-assembling protein-DNA nanowires
Components
  • DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3')
  • dualENH
Keywordsde novo design/DNA / helix-turn-helix / DNA-binding protein / double-stranded DNA / de novo design-DNA complex
Function / homologyHomeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / DNA / DNA (> 10)
Function and homology information
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMou, Y. / Mayo, S.L.
CitationJournal: Nature / Year: 2015
Title: Computational design of co-assembling protein-DNA nanowires.
Authors: Mou, Y. / Yu, J.Y. / Wannier, T.M. / Guo, C.L. / Mayo, S.L.
History
DepositionJul 8, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Sep 30, 2015Group: Database references
Revision 1.3Sep 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
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: dualENH
B: dualENH
C: dualENH
D: dualENH
E: DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3')
G: DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3')
F: DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3')
H: DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)54,3208
Polymers54,3208
Non-polymers00
Water0
1
A: dualENH
B: dualENH
E: DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3')
F: DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,1604
Polymers27,1604
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-31 kcal/mol
Surface area12430 Å2
MethodPISA
2
C: dualENH
D: dualENH
G: DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3')
H: DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3')


Theoretical massNumber of molelcules
Total (without water)27,1604
Polymers27,1604
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-34 kcal/mol
Surface area12610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.098, 90.098, 158.923
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

#1: Protein
dualENH


Mass: 8683.909 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: A computationally designed protein using wild-type engrailed homeodomain as the backbone template
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli)
#2: DNA chain DNA (5'-D(P*GP*TP*GP*TP*AP*AP*TP*TP*TP*AP*AP*TP*TP*TP*CP*C)-3')


Mass: 4878.187 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: A short NA strand with engrailed homeodomain binding motifs
#3: DNA chain DNA (5'-D(P*CP*GP*GP*AP*AP*AP*TP*TP*AP*AP*AP*TP*TP*AP*CP*A)-3')


Mass: 4914.243 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: A short NA strand with engrailed homeodomain binding motifs

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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: 2.97 Å3/Da / Density % sol: 58.57 %
Crystal growTemperature: 298 K / pH: 7
Details: 800 mM, NaCl, 0.2 M Potassium thiocyanate, 20% w/v polyethylene glycerol 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2014
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.1→39.2 Å / Num. obs: 15510 / Redundancy: 10.7 % / Rsym value: 0.022 / Net I/σ(I): 102.5
Reflection shellResolution: 2.86→3.02 Å / Redundancy: 9.7 % / Rsym value: 6.972 / % possible all: 88.5

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASESphasing
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HHD

3hhd


Resolution: 3.2→36.35 Å / SU ML: 0.58 / σ(F): 1.35 / Phase error: 39.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.322 1136 10.01 %
Rwork0.264 --
obs0.27 11351 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→36.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1610 1293 0 0 2903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123110
X-RAY DIFFRACTIONf_angle_d1.324496
X-RAY DIFFRACTIONf_dihedral_angle_d26.7451133
X-RAY DIFFRACTIONf_chiral_restr0.061499
X-RAY DIFFRACTIONf_plane_restr0.01361
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2003-3.34590.49431370.3991237X-RAY DIFFRACTION100
3.3459-3.52220.41521380.33921235X-RAY DIFFRACTION99
3.5222-3.74260.40991380.36121250X-RAY DIFFRACTION100
3.7426-4.03130.37491390.32941246X-RAY DIFFRACTION100
4.0313-4.43630.32821410.29741268X-RAY DIFFRACTION100
4.4363-5.07680.3561430.28341287X-RAY DIFFRACTION100
5.0768-6.39050.33071450.29591304X-RAY DIFFRACTION100
6.3905-36.35540.27221550.20291388X-RAY DIFFRACTION100
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)
14.84243.4345-0.44532.32890.11130.5635-2.27261.9566-3.4554-1.3087-0.46011.07180.3278-1.14970.6830.8714-0.232-0.56922.83550.03682.248912.823880.93952.9441
20.63012.2098-1.78096.6884-6.44316.6730.9503-0.7099-0.0598-0.290.7798-1.5593-0.8171-2.8902-1.69171.01050.3861-0.32262.77750.41181.744415.597883.73877.4731
34.4183-1.5331-0.76215.4731-0.98754.4672-0.99040.434-0.9566-1.4210.75381.5284-1.04310.7699-0.07851.2834-0.1069-0.41111.64480.15671.551537.830973.291731.5231
41.9376-0.74340.57370.37080.38297.66170.39461.1240.2965-0.3019-0.76250.5048-0.5809-0.36860.16891.3555-0.1504-0.12771.28940.12881.084640.987274.779226.5573
54.1597-1.60140.47841.70390.51260.80340.50533.0494-3.3075-2.24772.0670.9459-0.75860.01750.27841.3772-0.60310.17780.9809-0.08091.500339.645961.17352.4584
61.649-2.20871.19673.3632-0.32364.9860.5131-0.2978-0.7120.225-0.7415-0.3605-0.8656-1.35630.28022.38830.6643-0.2209-1.00920.12231.551944.072565.380340.7549
72.6943-1.15662.17233.151-4.73087.2781.9341-0.91230.2870.7919-2.1132-1.523-1.88921.3435-0.07382.61490.2521-0.47750.8631-0.29651.379747.104875.57545.1071
83.2838-1.19640.49790.48660.11013.1769-1.16-0.26722.8486-0.43521.2007-0.4004-2.9386-0.57670.02451.9804-0.1127-0.01141.11570.3161.107337.410672.060848.4134
98.508-4.11230.64777.821.16331.97140.0837-1.86770.2416-0.49081.5294-0.8931.90120.3457-0.01371.9452-0.0358-0.46880.8774-0.13380.877652.656464.116748.0748
102.1973-3.44530.32965.77780.56393.2168-0.5520.32181.27331.37490.4673-2.6154-1.2811.08220.24711.985-0.02070.08760.9204-0.00661.485450.728876.34873.5199
118.50762.2043-2.56792.2182-1.44741.2120.74591.3983-0.28371.37570.4965-2.13323.40641.6734-0.75611.94710.4547-0.36521.0564-0.18661.034741.572173.085669.6837
121.4529-1.1545-0.4211.45160.68452.5326-1.19360.6752-1.35050.10611.34620.2136-0.82910.1701-0.47551.6227-0.13970.14221.0498-0.28271.029855.981874.102868.1762
134.484-1.2269-0.24040.634-0.39820.69020.3509-2.0717-3.16671.49330.53120.78181.8354-2.6937-0.6211.8291-0.51860.08772.09730.40431.94413.413369.954117.103
143.21070.2821-0.09743.378-1.11124.64-0.7881-0.7944-0.13730.3017-0.3839-1.17080.4842-1.67460.73491.7812-0.4615-0.28542.11540.23151.623535.21680.76213.3572
152.84940.7892.52727.16411.73236.31610.9746-0.7343-0.5789-0.63870.2037-1.0367-1.1268-0.9649-0.58162.3631-0.07770.03822.20980.08451.720835.943485.427717.3923
164.8220.1027-1.06853.5157-1.03695.0525-1.78682.3479-1.1772-1.09250.9274-0.6721-0.5712-0.42370.22362.8452-0.3628-0.06961.8185-0.07082.13517.116469.057318.3217
172.86781.23732.13183.5731.78863.66571.2956-1.288-0.05850.8207-1.8576-0.15730.0726-0.32760.45511.7467-0.1166-0.22071.2105-0.04511.668556.241666.333856.8096
184.2727-2.91222.15263.53770.2651.3432-0.596-0.55320.0661-0.58060.0218-0.7472-0.41640.51930.50952.4265-0.2079-0.21061.69710.16571.65857.394469.536559.604
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 27 )
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 59 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 27 )
4X-RAY DIFFRACTION4chain 'B' and (resid 28 through 59 )
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 9 )
6X-RAY DIFFRACTION6chain 'C' and (resid 10 through 22 )
7X-RAY DIFFRACTION7chain 'C' and (resid 23 through 35 )
8X-RAY DIFFRACTION8chain 'C' and (resid 36 through 41 )
9X-RAY DIFFRACTION9chain 'C' and (resid 42 through 61 )
10X-RAY DIFFRACTION10chain 'D' and (resid 5 through 27 )
11X-RAY DIFFRACTION11chain 'D' and (resid 28 through 41 )
12X-RAY DIFFRACTION12chain 'D' and (resid 42 through 59 )
13X-RAY DIFFRACTION13chain 'E' and (resid 1 through 9 )
14X-RAY DIFFRACTION14chain 'E' and (resid 10 through 15 )
15X-RAY DIFFRACTION15chain 'F' and (resid 1 through 8 )
16X-RAY DIFFRACTION16chain 'F' and (resid 9 through 16 )
17X-RAY DIFFRACTION17chain 'G' and (resid 1 through 16 )
18X-RAY DIFFRACTION18chain 'H' and (resid 1 through 16 )

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