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Yorodumi- PDB-2waq: The complete structure of the archaeal 13-subunit DNA-directed RN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2waq | ||||||
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Title | The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase | ||||||
Components | (DNA-DIRECTED RNA POLYMERASE ...) x 13 | ||||||
Keywords | TRANSCRIPTION / MULTI-SUBUNIT / RNA POLYMERASE | ||||||
Function / homology | Function and homology information 3 iron, 4 sulfur cluster binding / RNA polymerase III activity / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase ...3 iron, 4 sulfur cluster binding / RNA polymerase III activity / RNA polymerase II activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / DNA-templated transcription / nucleotide binding / magnesium ion binding / DNA binding / zinc ion binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | SULFOLOBUS SHIBATAE (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å | ||||||
Authors | Korkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G.A. | ||||||
Citation | Journal: Plos Biol. / Year: 2009 Title: Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure. Authors: Korkhin, Y. / Unligil, U.M. / Littlefield, O. / Nelson, P.J. / Stuart, D.I. / Sigler, P.B. / Bell, S.D. / Abrescia, N.G. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BJ" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2waq.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2waq.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 2waq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2waq_validation.pdf.gz | 563.6 KB | Display | wwPDB validaton report |
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Full document | 2waq_full_validation.pdf.gz | 629.8 KB | Display | |
Data in XML | 2waq_validation.xml.gz | 112.2 KB | Display | |
Data in CIF | 2waq_validation.cif.gz | 150.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wa/2waq ftp://data.pdbj.org/pub/pdb/validation_reports/wa/2waq | HTTPS FTP |
-Related structure data
Related structure data | 2wb1C 1en0 C: citing same article (ref.) 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
-DNA-DIRECTED RNA POLYMERASE ... , 13 types, 13 molecules ABCDEFGHKLNPQ
#1: Protein | Mass: 99766.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB53*PLUS |
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#2: Protein | Mass: 127582.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB55*PLUS |
#3: Protein | Mass: 43779.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) |
#4: Protein | Mass: 30179.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB56*PLUS |
#5: Protein | Mass: 20324.691 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) |
#6: Protein | Mass: 12822.612 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB58*PLUS |
#7: Protein | Mass: 15139.458 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB59*PLUS |
#8: Protein | Mass: 9688.296 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB60*PLUS |
#9: Protein | Mass: 10799.589 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) |
#10: Protein | Mass: 10211.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB62*PLUS |
#11: Protein | Mass: 7617.085 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB63*PLUS |
#12: Protein/peptide | Mass: 5606.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) |
#13: Protein | Mass: 12168.646 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) |
-Non-polymers , 3 types, 11 molecules
#14: Chemical | ChemComp-ZN / #15: Chemical | ChemComp-MG / | #16: Chemical | ChemComp-F3S / | |
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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: 3.6 Å3/Da / Density % sol: 66 % Description: THE STATISTICS FOR THIS DATA ARE DERIVED FROM MERGED IOBS AND SIGMAIOBS PRESENT IN THE ONLY MTZ AVAILABLE. RAW IMAGES COLLECTED IN 2001-2002 AND PROCESSING LOG-FILES HAVE BEEN LOST. |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: 7MG/ML ENZYME, 150MM KCL, 100MM SRCL2, 1MM ZNCL2, 100MM CACODYLATE PH 6.5, 12% PEG MME 5K, 5% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→42.8 Å / Num. obs: 59401 / % possible obs: 77 % / Observed criterion σ(I): -3 / Net I/σ(I): 8.5 |
Reflection shell | Highest resolution: 3.35 Å / Mean I/σ(I) obs: 1.7 / % possible all: 44.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EN0 1en0 Resolution: 3.35→42.78 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.769 / SU B: 87.522 / SU ML: 0.652 / Cross valid method: THROUGHOUT / ESU R Free: 0.869 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE REFINEMENT HAS ALSO BEEN CARRIED OUT USING NORMAL-MODE TO ANISOTROPICALLY REFINE THE OVERALL THERMAL MOTIONS. PLEASE SEE ARTICLE FOR MORE DETAILS.
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.76 Å2
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Refinement step | Cycle: LAST / Resolution: 3.35→42.78 Å
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Refine LS restraints |
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