+Open data
-Basic information
Entry | Database: PDB / ID: 5a1h | ||||||
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Title | Crystal structure of human Spindlin3 | ||||||
Components | SPINDLIN-3 | ||||||
Keywords | CELL CYCLE | ||||||
Function / homology | Spindlin/spermiogenesis-specific protein / Spindlin/spermiogenesis-specific domain superfamily / Spin/Ssty Family / gamete generation / methylated histone binding / regulation of DNA-templated transcription / nucleoplasm / cytosol / Spindlin-3 Function and homology information | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Srikannathasan, V. / Gileadi, C. / Johansson, C. / Shrestha, L. / Tallon, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Human Spindlin3 Authors: Srikannathasan, V. / Gileadi, C. / Johansson, C. / Shrestha, L. / Tallon, R. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Bountra, C. / Edwards, A. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5a1h.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5a1h.ent.gz | 135.5 KB | Display | PDB format |
PDBx/mmJSON format | 5a1h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5a1h_validation.pdf.gz | 452.7 KB | Display | wwPDB validaton report |
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Full document | 5a1h_full_validation.pdf.gz | 457.8 KB | Display | |
Data in XML | 5a1h_validation.xml.gz | 34.2 KB | Display | |
Data in CIF | 5a1h_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/5a1h ftp://data.pdbj.org/pub/pdb/validation_reports/a1/5a1h | HTTPS FTP |
-Related structure data
Related structure data | 4ns2S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 25548.750 Da / Num. of mol.: 4 / Fragment: RESIDUES 45-258 IS PEPTIDE BINDING DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q5JUX0 #2: Water | ChemComp-HOH / | Sequence details | HISTIDINE TAG CLEAVED, THE NUMBERING START AT 47 CHAIN A, B AND D, CHAIN C STARTS AT 46. AT THE C- ...HISTIDINE TAG CLEAVED, THE NUMBERING START AT 47 CHAIN A, B AND D, CHAIN C STARTS AT 46. AT THE C-TERMINAL CHAINS ABCD HAVE EXTRA RESIDUES FROM THE EXPRESSION | |
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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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: TWINNED DATA |
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Crystal grow | pH: 9 / Details: 0.1M TRIS PH 8.4, 38% PEG3350 |
-Data collection
Diffraction | Mean temperature: 287 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2015 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2→2.11 Å / Num. obs: 67153 / % possible obs: 99.7 % / Observed criterion σ(I): 3.1 / Redundancy: 7.6 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.7 | |||||||||||||||
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.1 / % possible all: 99.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4NS2 Resolution: 2→26.14 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.247 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.525 Å2
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Refinement step | Cycle: LAST / Resolution: 2→26.14 Å
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Refine LS restraints |
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