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- PDB-9d2x: SpiD ETS-domain (168-273) in complex with the DNA sequence d(AATA... -

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Basic information

Entry
Database: PDB / ID: 9d2x
TitleSpiD ETS-domain (168-273) in complex with the DNA sequence d(AATAAAAGGAAGTGGG)
Components
  • DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
  • DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
  • SpiD
KeywordsTRANSCRIPTION/DNA / transcription factor / protein-DNA complex / ETS family / ETS / PU.1 / TRANSCRIPTION-DNA complex / TRANSCRIPTION
Function / homology
Function and homology information


sequence-specific DNA binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / nucleus
Similarity search - Function
Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / SpiD
Similarity search - Component
Biological speciesRaja eglanteria (clearnose skate)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsTerrell, J.R. / Vernon, T.N. / Poon, G.M.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL155178 United States
National Science Foundation (NSF, United States)MCB2028902 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137160 United States
CitationJournal: To be published
Title: The Structure of the DNA-binding Domain of the Class III ETS-Family Member SpiD from Raja eglanteria
Authors: Terrell, J.R. / Vernon, T.N. / Poon, G.M.K.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
F: SpiD
A: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
B: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
E: SpiD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6327
Polymers45,3946
Non-polymers2381
Water79344
1
C: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
D: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
F: SpiD


Theoretical massNumber of molelcules
Total (without water)22,6973
Polymers22,6973
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')
B: DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')
E: SpiD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9354
Polymers22,6973
Non-polymers2381
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.934, 42.939, 62.534
Angle α, β, γ (deg.)79.209, 81.529, 76.185
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "C"
d_1ens_2(chain "B" and resid 17 through 32)
d_2ens_2chain "D"
d_1ens_3(chain "E" and (resid 169 through 180 or (resid 181...
d_2ens_3(chain "F" and (resid 169 through 185 or (resid 186...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1DADADGDGAD1 - 81 - 8
d_2ens_1DADADGDGCA1 - 81 - 8
d_1ens_2DTDTDTDTBE171
d_2ens_2DTDTDTDTDB171
d_1ens_3LYSLYSLEULEUEF169 - 2566 - 93
d_2ens_3LYSLYSLEULEUFC169 - 2566 - 93

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(0.15956437626, 0.622034393903, -0.766558818768), (0.355121249336, -0.760693791631, -0.543354261641), (-0.921101573171, -0.185521341564, -0.342277261479)-8.18748546142, -26.4908540132, -23.2481550824
2given(0.0988348481796, 0.564859708768, -0.819246716317), (0.41238473029, -0.772505204921, -0.482881499535), (-0.905632655666, -0.290119316454, -0.309289953298)-11.3282384599, -24.0660363556, -24.4943069345
3given(0.169100904478, 0.561754631147, -0.809837402501), (0.492887326731, -0.759744392348, -0.424087893536), (-0.853502763471, -0.32744494603, -0.405355202342)-10.7812637001, -21.6799277134, -28.2596442761

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Components

#1: DNA chain DNA (5'-D(*AP*AP*TP*AP*AP*AP*AP*GP*GP*AP*AP*GP*TP*GP*GP*G)-3')


Mass: 5044.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(*TP*CP*CP*CP*AP*CP*TP*TP*CP*CP*TP*TP*TP*TP*AP*T)-3')


Mass: 4750.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Protein SpiD


Mass: 12902.399 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Raja eglanteria (clearnose skate) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DEW5
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.07 Å3/Da / Density % sol: 40.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Looped directly from Index HT (Hampton Research) condition F12 from a robot screen - 200 mM NaCl, 100 mM HEPES, pH=7.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920119 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 15, 2022
RadiationMonochromator: vertical DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920119 Å / Relative weight: 1
ReflectionResolution: 2.29→32.35 Å / Num. obs: 15141 / % possible obs: 91.92 % / Redundancy: 1.7 % / Biso Wilson estimate: 45.81 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.03905 / Rpim(I) all: 0.03905 / Rrim(I) all: 0.05522 / Net I/σ(I): 11.02
Reflection shellResolution: 2.29→2.372 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.3318 / Mean I/σ(I) obs: 2.19 / Num. unique obs: 1543 / CC1/2: 0.854 / CC star: 0.96 / Rpim(I) all: 0.3318 / Rrim(I) all: 0.4692 / % possible all: 93.11

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→32.35 Å / SU ML: 0.3536 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.3408
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2702 1509 10.01 %
Rwork0.2207 13568 -
obs0.2256 15077 91.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.73 Å2
Refinement stepCycle: LAST / Resolution: 2.29→32.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1472 1300 15 44 2831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01242973
X-RAY DIFFRACTIONf_angle_d0.86294257
X-RAY DIFFRACTIONf_chiral_restr0.0403453
X-RAY DIFFRACTIONf_plane_restr0.0071311
X-RAY DIFFRACTIONf_dihedral_angle_d23.93011214
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2DAX-RAY DIFFRACTIONTorsion NCS1.1516198759
ens_2d_2EBX-RAY DIFFRACTIONTorsion NCS1.56303375668
ens_3d_2FEX-RAY DIFFRACTIONTorsion NCS1.26091830806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.360.32151400.29521258X-RAY DIFFRACTION93.32
2.36-2.450.34891400.29551260X-RAY DIFFRACTION93.9
2.45-2.550.36181390.29221246X-RAY DIFFRACTION93.64
2.55-2.660.35371420.30041281X-RAY DIFFRACTION94.87
2.66-2.80.36681410.29961264X-RAY DIFFRACTION95.06
2.8-2.980.36541400.29451267X-RAY DIFFRACTION94.18
2.98-3.210.30441340.26851216X-RAY DIFFRACTION91.65
3.21-3.530.27661350.21651201X-RAY DIFFRACTION89.07
3.53-4.040.25621340.20281192X-RAY DIFFRACTION88.7
4.04-5.090.20581300.17761182X-RAY DIFFRACTION87.99
5.09-32.350.211340.16151201X-RAY DIFFRACTION89.18
Refinement TLS params.Method: refined / Origin x: 0.606883705746 Å / Origin y: -7.04124576259 Å / Origin z: -19.2550655523 Å
111213212223313233
T0.23363447757 Å20.0300172609498 Å20.0261013849355 Å2-0.37867631175 Å20.0698817617099 Å2--0.359687160284 Å2
L0.900850931302 °20.915057934445 °20.316708008484 °2-1.57101625049 °20.799920548882 °2--1.59086843457 °2
S-0.0344619681392 Å °-0.00997905148723 Å °0.0097233075956 Å °0.012757883136 Å °0.00996969258663 Å °0.056463288133 Å °0.0149226771277 Å °0.0781758867125 Å °0.0386946911202 Å °
Refinement TLS groupSelection details: all

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