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Yorodumi- PDB-4v4g: Crystal structure of five 70s ribosomes from Escherichia Coli in ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4v4g | |||||||||
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Title | Crystal structure of five 70s ribosomes from Escherichia Coli in complex with protein Y. | |||||||||
Components |
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Keywords | RIBOSOME / 30S RIBOSOMAL SUBUNIT / PROTEIN-RNA COMPLEX / PROTEIN-PROTEIN COMPLEX / RNA-RNA COMPLEX | |||||||||
Function / homology | RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 11.5 Å | |||||||||
Authors | Vila-Sanjurjo, A. / Schuwirth, B.S. / Hau, C.W. / Cate, J.H. | |||||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2004 Title: Structural basis for the control of translation initiation during stress. Authors: Vila-Sanjurjo, A. / Schuwirth, B.S. / Hau, C.W. / Cate, J.H. | |||||||||
History |
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Remark 400 | COMPOUND THIS FILE, 1VOQ, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL ...COMPOUND THIS FILE, 1VOQ, CONTAINS THE 30S SUBUNIT OF ONE 70S RIBOSOME. THE ENTIRE CRYSTAL STRUCTURE CONTAINS FIVE 70S RIBOSOMES AND ARE DEPOSITED UNDER: 70S RIBOSOME ONE: 1VOQ (30S SUBUNIT), 1VOR (50S SUBUNIT) 70S RIBOSOME TWO: 1VOS (30S SUBUNIT), 1VOU (50S SUBUNIT) 70S RIBOSOME THREE: 1VOV (30S SUBUNIT), 1VOW (50S SUBUNIT) 70S RIBOSOME FOUR: 1VOX (30S SUBUNIT), 1VOY (50S SUBUNIT) 70S RIBOSOME FIVE: 1VOZ (30S SUBUNIT), 1VP0 (50S SUBUNIT) | |||||||||
Remark 999 | SEQUENCE The 30S subunit is modelled based on 1PNS which are derived mainly from 1J5E, the T. ...SEQUENCE The 30S subunit is modelled based on 1PNS which are derived mainly from 1J5E, the T. thermophilus 30S subunit, with modifications to the rRNA to make it match E. coli insertions and deletions. The sequence of this subunit represent that of pdb entry, 1J5E. As a result, no dbref was provided. Some residues are not at link distance. Distance of O3*-P bond is 3.20 for residue (A A 919 ) and residue (A U 920 ). Distance of O3*-P bond is 3.21 for residue (A U 1393 ) and residue (A A 1394 ). Distance of O3*-P bond is 5.27 for residue (A G 1443 ) and residue (A U 1445 ). Distance of O3*-P bond is 6.64 for residue (A G 1458 ) and residue (A A 1460 ). Distance of C-N bond is 5.58 for residue (L SER 22 ) and residue (L LYS 23 ). Distance of C-N bond is 4.55 for residue (M GLY 89 ) and residue (M LEU 90 ). The short contacts listed at remark 500 may not be complete since this file only represents one tenth of the entire crystal structure. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4v4g.cif.gz | 15.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb4v4g.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 4v4g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4v4g_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 4v4g_full_validation.pdf.gz | 9.9 MB | Display | |
Data in XML | 4v4g_validation.xml.gz | 1.9 MB | Display | |
Data in CIF | 4v4g_validation.cif.gz | 2.7 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v4/4v4g ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v4g | HTTPS FTP |
-Related structure data
Related structure data | 1pns 1pnu 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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2 |
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3 |
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4 |
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5 |
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Unit cell |
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-Components
-RNA chain , 3 types, 15 molecules AACAEAGAIABBDBFBHBJBBADAFAHAJA
#1: RNA chain | Mass: 495435.469 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #22: RNA chain | Mass: 915854.875 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #23: RNA chain | Mass: 38374.984 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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-30S ribosomal protein ... , 19 types, 95 molecules ABCBEBGBIBACCCECGCICADCDEDGDIDAECEEEGEIEAFCFEFGFIFAGCGEGGGIG...
#2: Protein | Mass: 26987.271 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #3: Protein | Mass: 22862.430 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #4: Protein | Mass: 24242.254 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #5: Protein | Mass: 16331.079 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #6: Protein | Mass: 11988.753 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #7: Protein | Mass: 17919.775 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #8: Protein | Mass: 15868.570 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #9: Protein | Mass: 14298.466 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #10: Protein | Mass: 11299.176 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #11: Protein | Mass: 12606.369 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #12: Protein | Mass: 13804.311 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #13: Protein | Mass: 14207.666 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #14: Protein | Mass: 7027.529 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #15: Protein | Mass: 10447.213 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #16: Protein | Mass: 9924.469 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #17: Protein | Mass: 12193.475 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #18: Protein | Mass: 8483.172 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #19: Protein | Mass: 9203.743 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #20: Protein | Mass: 10907.060 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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-Protein , 2 types, 10 molecules AaCaEaGaIaBWDWFWHWJW
#21: Protein | Mass: 10250.834 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) #43: Protein | Mass: 18929.711 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) |
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+50S ribosomal protein ... , 29 types, 145 molecules BDDDFDHDJDBEDEFEHEJEBFDFFFHFJFBGDGFGHGJGBHDHFHHHJHBIDIFIHIJI...
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 5.38 Å3/Da / Density % sol: 77.12 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 18-22% 2-methyl-2,4-pentanediol (MPD), 0-5% ethanol, 20-25mM MgCl2, 200-320mM NH4Cl, 1mM spermine, 0-0.5mM spermidine, pH 6.0-6.5, pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 11.5→500 Å / Num. obs: 62383 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Rsym value: 0.181 / Net I/σ(I): 7.4 | ||||||||||||||||||||
Reflection shell | Resolution: 11.5→11.8 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.462 / % possible all: 77.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1PNS, 1PNU Resolution: 11.5→500 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 Details: 235 RIGID BODIES REFINEMENT, GROUPED THIS ENTRY. COORDINATES USED FOR SOLVING AND REFINING THIS SUBUNIT COMES FROM PDB ENTRY, 1PNS, WHERE THE SEQUENCE REPRESENTS THAT OF T. THERMOPHILUS.
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Refinement step | Cycle: LAST / Resolution: 11.5→500 Å
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