+Open data
-Basic information
Entry | Database: PDB / ID: 7z8a | ||||||
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Title | Sam68 | ||||||
Components | KHDR1 protein | ||||||
Keywords | RNA BINDING PROTEIN / STAR | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Nadal, M. / Fuentes-Prior, P. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Protein Sci. / Year: 2023 Title: Structure and function analysis of Sam68 and hnRNP A1 synergy in the exclusion of exon 7 from SMN2 transcripts. Authors: Nadal, M. / Anton, R. / Dorca-Arevalo, J. / Estebanez-Perpina, E. / Tizzano, E.F. / Fuentes-Prior, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7z8a.cif.gz | 42.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7z8a.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7z8a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7z8a_validation.pdf.gz | 468.2 KB | Display | wwPDB validaton report |
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Full document | 7z8a_full_validation.pdf.gz | 468.7 KB | Display | |
Data in XML | 7z8a_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | 7z8a_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z8/7z8a ftp://data.pdbj.org/pub/pdb/validation_reports/z8/7z8a | HTTPS FTP |
-Related structure data
Related structure data | 7z89C 7z9aC 7z9bC 7zabC 7zacC 7zafC 7zamC 5emoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 13115.519 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Khdrbs1, MELVER_R13249 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7K8A7M1 |
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-Non-polymers , 5 types, 65 molecules
#2: Chemical | ChemComp-NO3 / #3: Chemical | ChemComp-LI / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.73 Å3/Da / Density % sol: 67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate 2 M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→48.53 Å / Num. obs: 12775 / % possible obs: 99.4 % / Redundancy: 9.1 % / CC1/2: 0.3 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.95→2.02 Å / Num. unique obs: 1402 / CC1/2: 0.406 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EMO Resolution: 2.06→48.53 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.346 / SU ML: 0.129 / Cross valid method: FREE R-VALUE / ESU R: 0.153 / ESU R Free: 0.151 / Details: Hydrogens have not been used
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.544 Å2
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Refinement step | Cycle: LAST / Resolution: 2.06→48.53 Å
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Refine LS restraints |
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LS refinement shell |
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