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- PDB-6sqt: Structure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant -

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Basic information

Entry
Database: PDB / ID: 6sqt
TitleStructure of the U1A variant A1-98 Y31H/Q36R/F56W triple mutant
ComponentsU1 small nuclear ribonucleoprotein A
KeywordsRNA BINDING PROTEIN / U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A / U1A / RNA hairpin / co-crystallization
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsRosenbach, H. / Span, I.
CitationJournal: J.Struct.Biol. / Year: 2020
Title: Expanding crystallization tools for nucleic acid complexes using U1A protein variants.
Authors: Rosenbach, H. / Victor, J. / Borggrafe, J. / Biehl, R. / Steger, G. / Etzkorn, M. / Span, I.
History
DepositionSep 4, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: U1 small nuclear ribonucleoprotein A
BBB: U1 small nuclear ribonucleoprotein A
CCC: U1 small nuclear ribonucleoprotein A


Theoretical massNumber of molelcules
Total (without water)34,1383
Polymers34,1383
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-11 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.810, 89.810, 86.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11AAA-127-

HOH

21CCC-122-

HOH

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Components

#1: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 11379.352 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Production host: Escherichia coli (E. coli) / References: UniProt: P09012
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2.2 M ammonium sulfate, 0.2 M tri-potassium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.84→38.89 Å / Num. obs: 29093 / % possible obs: 82.1 % / Redundancy: 13.9 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.056 / Net I/σ(I): 25.4
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 0.871 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 238 / CC1/2: 0.276 / Rrim(I) all: 1.189 / % possible all: 13.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→38.89 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.455 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.14
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2446 1474 5.071 %
Rwork0.2134 --
all0.215 --
obs-29067 82.004 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.399 Å2
Baniso -1Baniso -2Baniso -3
1--1.628 Å2-0.814 Å2-0 Å2
2---1.628 Å20 Å2
3---5.28 Å2
Refinement stepCycle: LAST / Resolution: 1.84→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2198 0 0 73 2271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132243
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172183
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.6493009
X-RAY DIFFRACTIONr_angle_other_deg1.3311.5835065
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1095265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.48221.176119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78115442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4321518
X-RAY DIFFRACTIONr_chiral_restr0.0780.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022417
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
X-RAY DIFFRACTIONr_nbd_refined0.1920.2395
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21897
X-RAY DIFFRACTIONr_nbtor_refined0.1620.21057
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0970.2995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.281
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2220.218
X-RAY DIFFRACTIONr_nbd_other0.2340.266
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.216
X-RAY DIFFRACTIONr_mcbond_it3.4433.9621069
X-RAY DIFFRACTIONr_mcbond_other3.4333.9611068
X-RAY DIFFRACTIONr_mcangle_it4.8055.9151331
X-RAY DIFFRACTIONr_mcangle_other4.8065.9181332
X-RAY DIFFRACTIONr_scbond_it4.3754.671174
X-RAY DIFFRACTIONr_scbond_other4.3734.6731175
X-RAY DIFFRACTIONr_scangle_it6.8326.7141678
X-RAY DIFFRACTIONr_scangle_other6.836.7171679
X-RAY DIFFRACTIONr_lrange_it8.70445.5862435
X-RAY DIFFRACTIONr_lrange_other8.71345.5732424
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.8880.449200.399458X-RAY DIFFRACTION18.3775
1.888-1.940.351500.375946X-RAY DIFFRACTION39.6971
1.94-1.9960.355700.3391290X-RAY DIFFRACTION54.9939
1.996-2.0570.274660.31549X-RAY DIFFRACTION67.9714
2.057-2.1250.275790.2671754X-RAY DIFFRACTION79.4883
2.125-2.1990.2891100.2451882X-RAY DIFFRACTION88.8889
2.199-2.2820.2471030.2191983X-RAY DIFFRACTION96.2177
2.282-2.3750.2371040.1981976X-RAY DIFFRACTION99.5692
2.375-2.4810.278870.2031902X-RAY DIFFRACTION99.7493
2.481-2.6020.236920.1911814X-RAY DIFFRACTION99.4781
2.602-2.7430.2751040.2121724X-RAY DIFFRACTION99.8362
2.743-2.9090.248930.2231644X-RAY DIFFRACTION99.4845
2.909-3.1090.284830.2321542X-RAY DIFFRACTION99.7545
3.109-3.3580.215590.2161458X-RAY DIFFRACTION100
3.358-3.6780.235760.191340X-RAY DIFFRACTION99.9294
3.678-4.1110.202880.1811181X-RAY DIFFRACTION100
4.111-4.7460.186460.161106X-RAY DIFFRACTION99.9133
4.746-5.8080.253610.218899X-RAY DIFFRACTION99.6885
5.808-8.1950.225620.241717X-RAY DIFFRACTION100
8.195-38.890.328210.251428X-RAY DIFFRACTION97.6087

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