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Yorodumi- PDB-4yu8: Crystal structure of Neuroblastoma suppressor of tumorigenicity 1 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yu8 | ||||||
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Title | Crystal structure of Neuroblastoma suppressor of tumorigenicity 1 | ||||||
Components | Neuroblastoma suppressor of tumorigenicity 1 | ||||||
Keywords | ANTITUMOR PROTEIN / BMP Binding Protein / NBL1 DAN domain family member 1 BMP-binding / Structural Genomics / Oxford Protein Production Facility / OPPF | ||||||
Function / homology | Function and homology information sequestering of BMP from receptor via BMP binding / sequestering of BMP in extracellular matrix / negative regulation of monocyte chemotaxis / determination of dorsal identity / morphogen activity / BMP binding / negative regulation of BMP signaling pathway / positive regulation of neuron differentiation / neuron projection morphogenesis / animal organ morphogenesis ...sequestering of BMP from receptor via BMP binding / sequestering of BMP in extracellular matrix / negative regulation of monocyte chemotaxis / determination of dorsal identity / morphogen activity / BMP binding / negative regulation of BMP signaling pathway / positive regulation of neuron differentiation / neuron projection morphogenesis / animal organ morphogenesis / nervous system development / receptor ligand activity / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Ren, J. / Nettleship, J.E. / Stammers, D.K. / Owens, R.J. / Oxford Protein Production Facility (OPPF) | ||||||
Citation | Journal: To Be Published Title: Crystal structure of Neuroblastoma suppressor of tumorigenicity 1 Authors: Ren, J. / Nettleship, J.E. / Stammers, D.K. / Owens, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yu8.cif.gz | 48.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yu8.ent.gz | 32.3 KB | Display | PDB format |
PDBx/mmJSON format | 4yu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yu8_validation.pdf.gz | 456.1 KB | Display | wwPDB validaton report |
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Full document | 4yu8_full_validation.pdf.gz | 456.4 KB | Display | |
Data in XML | 4yu8_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | 4yu8_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yu/4yu8 ftp://data.pdbj.org/pub/pdb/validation_reports/yu/4yu8 | HTTPS FTP |
-Related structure data
Related structure data | 4x1jS 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
#1: Protein | Mass: 15110.457 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NBL1, DAN, DAND1 / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P41271 |
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#2: Chemical | ChemComp-GOL / |
#3: Sugar | ChemComp-NAG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.68 Å3/Da / Density % sol: 26.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG3350 25 %w/v, Magnesium Chloride 0.2M, bis-Tris 0.1M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.278 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.278 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. obs: 10031 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 18.2 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 59 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4x1j Resolution: 1.8→42.62 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.111 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.123 / 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: 40.872 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→42.62 Å
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Refine LS restraints |
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