+Open data
-Basic information
Entry | Database: PDB / ID: 1nmu | |||||||||
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Title | MBP-L30 | |||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN/RIBOSOME / structural flexibility / ribosomal protein L30 / MBP-L30 fusion protein / SUGAR BINDING PROTEIN-RIBOSOME COMPLEX | |||||||||
Function / homology | Function and homology information pre-mRNA 5'-splice site binding / detection of maltose stimulus / maltose transport complex / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / carbohydrate transport / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome ...pre-mRNA 5'-splice site binding / detection of maltose stimulus / maltose transport complex / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / carbohydrate transport / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / rRNA processing / outer membrane-bounded periplasmic space / cytosolic large ribosomal subunit / cytoplasmic translation / periplasmic space / structural constituent of ribosome / DNA damage response / RNA binding / membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | |||||||||
Authors | Chao, J.A. / Prasad, G.S. / White, S.A. / Stout, C.D. / Williamson, J.R. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Inherent Protein Structural Flexibility at the RNA-binding Interface of L30e Authors: Chao, J.A. / Prasad, G.S. / White, S.A. / Stout, C.D. / Williamson, J.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1nmu.cif.gz | 194.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1nmu.ent.gz | 155.5 KB | Display | PDB format |
PDBx/mmJSON format | 1nmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1nmu_validation.pdf.gz | 519.2 KB | Display | wwPDB validaton report |
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Full document | 1nmu_full_validation.pdf.gz | 552.9 KB | Display | |
Data in XML | 1nmu_validation.xml.gz | 23.6 KB | Display | |
Data in CIF | 1nmu_validation.cif.gz | 36 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/1nmu ftp://data.pdbj.org/pub/pdb/validation_reports/nm/1nmu | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 41841.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P02928, UniProt: P0AEX9*PLUS #2: Protein | Mass: 11299.168 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P14120 #3: Polysaccharide | #4: 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: 3.41 Å3/Da / Density % sol: 63.92 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Sodium Citrate, Tris, Sodium Chloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / pH: 6.2 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2000 / Details: double crystal monochromater |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→18 Å / Num. all: 65857 / Num. obs: 65330 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.31→2.38 Å / % possible all: 99.8 |
Reflection | *PLUS Lowest resolution: 18 Å / Num. measured all: 708695 / Rmerge(I) obs: 0.086 |
Reflection shell | *PLUS % possible obs: 99.8 % / Rmerge(I) obs: 0.359 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→18 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.31→18 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 18 Å / Rfactor Rfree: 0.2544 / Rfactor Rwork: 0.2225 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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