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Yorodumi- PDB-6nyq: Crystal structure of glycosylated lysosomal membrane protein (GLM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nyq | ||||||
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Title | Crystal structure of glycosylated lysosomal membrane protein (GLMP) luminal domain bound to a Fab fragment | ||||||
Components |
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Keywords | IMMUNE SYSTEM / lysosome / luminal domain | ||||||
Function / homology | Function and homology information protein localization to lysosome / lysosome / protein stabilization / lysosomal membrane / positive regulation of transcription by RNA polymerase II / membrane / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Huang, C.S. / Boenig, G. / Hymowitz, S.G. | ||||||
Citation | Journal: To Be Published Title: GLMP is essential for bone-marrow hematopoiesis and lysosomal glycolipid metabolism Authors: Manzanillo, P. / Huang, C.S. / Boenig, G. / Calses, P. / Scherl, A. / Reichelt, M. / Katakam, A.K. / Martin, F. / Hymowitz, S.G. / Ouyang, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nyq.cif.gz | 170.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nyq.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 6nyq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6nyq_validation.pdf.gz | 463 KB | Display | wwPDB validaton report |
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Full document | 6nyq_full_validation.pdf.gz | 468.4 KB | Display | |
Data in XML | 6nyq_validation.xml.gz | 35.4 KB | Display | |
Data in CIF | 6nyq_validation.cif.gz | 52.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ny/6nyq ftp://data.pdbj.org/pub/pdb/validation_reports/ny/6nyq | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Antibody , 2 types, 2 molecules LH
#1: Antibody | Mass: 23570.184 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
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#2: Antibody | Mass: 24067.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) |
-Protein / Sugars , 2 types, 7 molecules C
#3: Protein | Mass: 43831.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Glmp / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JHJ3 |
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#5: Sugar | ChemComp-NAG / |
-Non-polymers , 2 types, 632 molecules
#4: Chemical | ChemComp-NA / #6: 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: 2.43 Å3/Da / Density % sol: 49.42 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / Details: 8% tacsimate pH 6.0, 16% PEG 3350, 10 mM phenol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→30 Å / Num. obs: 71330 / % possible obs: 99.8 % / Redundancy: 3.3 % / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.97 / CC1/2: 0.611 / Rsym value: 0.672 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.985 / SU ML: 0.088 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.114 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.376 Å2
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Refinement step | Cycle: 1 / Resolution: 1.85→30 Å
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Refine LS restraints |
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