+Open data
-Basic information
Entry | Database: PDB / ID: 7e9m | ||||||
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Title | Crystal Structure of Spindlin1 bound to SPINDOC Docpep3 | ||||||
Components |
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Keywords | TRANSCRIPTION / Spin/Ssty repeat | ||||||
Function / homology | Function and homology information regulation of protein ADP-ribosylation / gamete generation / site of DNA damage / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization ...regulation of protein ADP-ribosylation / gamete generation / site of DNA damage / rRNA transcription / positive regulation of Wnt signaling pathway / methylated histone binding / meiotic cell cycle / Wnt signaling pathway / spindle / chromatin organization / nuclear membrane / negative regulation of DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / nucleolus / positive regulation of DNA-templated transcription / nucleoplasm / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Zhao, F. / Li, H. | ||||||
Citation | Journal: to be published Title: Molecular basis for SPINDOC-Spindlin1 engagement and its role in transcriptional inhibition Authors: Zhao, F. / Li, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7e9m.cif.gz | 106.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7e9m.ent.gz | 78.7 KB | Display | PDB format |
PDBx/mmJSON format | 7e9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7e9m_validation.pdf.gz | 447.6 KB | Display | wwPDB validaton report |
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Full document | 7e9m_full_validation.pdf.gz | 454.6 KB | Display | |
Data in XML | 7e9m_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 7e9m_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/7e9m ftp://data.pdbj.org/pub/pdb/validation_reports/e9/7e9m | HTTPS FTP |
-Related structure data
Related structure data | 7ea1C 2ns2S 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 29644.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPIN1, OCR, SPIN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9Y657 #2: Protein/peptide | Mass: 2953.287 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SPINDOC, C11orf84 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BUA3 #3: Water | ChemComp-HOH / | |
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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: 2.33 Å3/Da / Density % sol: 47.15 % / Mosaicity: 0.567 ° / Mosaicity esd: 0.017 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 0.2M magnesium acetate, 0.1M Sodium cacodylate pH 6.5, 20% PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97921 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2020 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97921 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.5→50 Å / Num. obs: 20960 / % possible obs: 99.4 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.079 / Rrim(I) all: 0.137 / Χ2: 0.934 / Net I/σ(I): 5.9 / Num. measured all: 61133 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2NS2 Resolution: 2.5→38.75 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.78 / 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: 134.16 Å2 / Biso mean: 43.0809 Å2 / Biso min: 16.09 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.5→38.75 Å
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7
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