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Yorodumi- PDB-1xmq: Crystal Structure of t6A37-ASLLysUUU AAA-mRNA Bound to the Decodi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xmq | ||||||
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Title | Crystal Structure of t6A37-ASLLysUUU AAA-mRNA Bound to the Decoding Center | ||||||
Components |
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Keywords | RIBOSOME / decoding / modified tRNA | ||||||
Function / homology | Function and homology information ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex ...ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / zinc ion binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Murphy, F.V. / Ramakrishnan, V. / Malkiewicz, A. / Agris, P.F. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: The role of modifications in codon discrimination by tRNA(Lys)(UUU). Authors: Murphy, F.V. / Ramakrishnan, V. / Malkiewicz, A. / Agris, P.F. | ||||||
History |
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Remark 999 | SEQUENCE Residues G1002 and G1003; G1031 and 1032; C1362 and A1363; C1539 and U1540 in chain A are ...SEQUENCE Residues G1002 and G1003; G1031 and 1032; C1362 and A1363; C1539 and U1540 in chain A are linked together which are shown as close contacts at remark 500. The missing residues within the links are listed in remark 465. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xmq.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1xmq.ent.gz | 938.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1xmq_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1xmq_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 1xmq_validation.xml.gz | 148.3 KB | Display | |
Data in CIF | 1xmq_validation.cif.gz | 211.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xm/1xmq ftp://data.pdbj.org/pub/pdb/validation_reports/xm/1xmq | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-RNA chain , 3 types, 3 molecules AWX
#1: RNA chain | Mass: 493958.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: GenBank: 155076 |
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#2: RNA chain | Mass: 1271.866 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: RNA chain | Mass: 3574.172 Da / Num. of mol.: 1 / Source method: obtained synthetically |
-30S Ribosomal Protein ... , 20 types, 20 molecules BCDEFGHIJKLMNOPQRSTV
#4: Protein | Mass: 29317.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80371 |
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#5: Protein | Mass: 26751.076 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80372 |
#6: Protein | Mass: 24373.447 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80373 |
#7: Protein | Mass: 17583.416 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P27152, UniProt: Q5SHQ5*PLUS |
#8: Protein | Mass: 11988.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P23370, UniProt: Q5SLP8*PLUS |
#9: Protein | Mass: 18050.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P17291 |
#10: Protein | Mass: 15868.570 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62668, UniProt: P0DOY9*PLUS |
#11: Protein | Mass: 14429.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80374 |
#12: Protein | Mass: 11954.968 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80375, UniProt: Q5SHN7*PLUS |
#13: Protein | Mass: 13737.868 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80376 |
#14: Protein | Mass: 14920.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: GenBank: 581812, UniProt: Q5SHN3*PLUS |
#15: Protein | Mass: 14338.861 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80377 |
#16: Protein | Mass: 7158.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P24320, UniProt: P0DOY6*PLUS |
#17: Protein | Mass: 10578.407 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80378, UniProt: Q5SJ76*PLUS |
#18: Protein | Mass: 10409.983 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80379, UniProt: Q5SJH3*PLUS |
#19: Protein | Mass: 12324.670 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62658, UniProt: P0DOY7*PLUS |
#20: Protein | Mass: 10244.272 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80382, UniProt: Q5SLQ0*PLUS |
#21: Protein | Mass: 10605.464 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80381, UniProt: Q5SHP2*PLUS |
#22: Protein | Mass: 11736.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P80380 |
#23: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / References: UniProt: P62612, UniProt: Q5SIH3*PLUS |
-Non-polymers , 3 types, 110 molecules
#24: Chemical | ChemComp-PAR / | ||
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#25: Chemical | ChemComp-MG / #26: Chemical | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.46 Å3/Da / Density % sol: 72.4 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: MPD, magnesium chloride, potassium chloride, ammonium chloride, MES-KOH, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.K | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 16, 2003 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 3→99 Å / Num. obs: 263974 / % possible obs: 97.4 % / Redundancy: 29.2 % / Rsym value: 0.142 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 3→3.11 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.722 / % possible all: 91.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: empty 30S Resolution: 3→99 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 77.07 Å2 | ||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→99 Å
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Refine LS restraints |
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