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Yorodumi- PDB-7lhx: Human U1A protein with F37M and F77M mutations for improved phasing -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lhx | |||||||||
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Title | Human U1A protein with F37M and F77M mutations for improved phasing | |||||||||
Components | U1 small nuclear ribonucleoprotein A | |||||||||
Keywords | RNA BINDING PROTEIN / RNA-LIGAND INTERACTIONS / RNA RECOGNITION MOTIF / RNA BINDING DOMAIN | |||||||||
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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Jenkins, J.L. / Lippa, G.M. / Wedekind, J.E. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Crystals / Year: 2021 Title: Affinity and Structural Analysis of the U1A RNA Recognition Motif with Engineered Methionines to Improve Experimental Phasing Authors: Srivastava, K.Y. / Bonn-Breach, R.B. / Chavali, S.S. / Lippa, G.M. / Jenkins, J.L. / Wedekind, J.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lhx.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lhx.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 7lhx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lh/7lhx ftp://data.pdbj.org/pub/pdb/validation_reports/lh/7lhx | HTTPS FTP |
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-Related structure data
Related structure data | 1urnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11636.626 Da / Num. of mol.: 1 / Mutation: Y31H, Q36R, F37M, F77M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P09012 | ||||||
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#2: Chemical | ChemComp-NA / | ||||||
#3: Chemical | #4: Chemical | ChemComp-BME / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 51.6 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.7-3.1 M Sodium Acetate / PH range: 6.5 to 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å |
Detector | Type: APEX II CCD / Detector: CCD / Date: Nov 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→27.88 Å / Num. obs: 10961 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 1 / Rmerge(I) obs: 0.029 / Rpim(I) all: 0.009 / Net I/σ(I): 61.2 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.076 / Mean I/σ(I) obs: 20.2 / Num. unique obs: 558 / CC1/2: 0.995 / Rpim(I) all: 0.038 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1urn Resolution: 2.2→27.88 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.56 Å2 / Biso mean: 23.322 Å2 / Biso min: 5.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→27.88 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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