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Yorodumi- PDB-2wb1: The complete structure of the archaeal 13-subunit DNA-directed RN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wb1 | ||||||
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Title | The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase | ||||||
Components |
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Keywords | TRANSCRIPTION / RNA-POLYMERASE / MULTI-SUBUNIT ENZYME | ||||||
Function / homology | Function and homology information RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / nucleotidyltransferase activity / DNA-templated transcription initiation ...RNA polymerase binding / 3 iron, 4 sulfur cluster binding / transcription initiation at RNA polymerase III promoter / RNA polymerase III activity / tRNA transcription by RNA polymerase III / RNA polymerase I activity / DNA-directed RNA polymerase complex / RNA polymerase II activity / nucleotidyltransferase activity / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / nucleotide binding / DNA-templated transcription / 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: 3.52 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 Polymerase: 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.A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET 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 | 2wb1.cif.gz | 2.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2wb1.ent.gz | 2.2 MB | Display | PDB format |
PDBx/mmJSON format | 2wb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wb1_validation.pdf.gz | 710.2 KB | Display | wwPDB validaton report |
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Full document | 2wb1_full_validation.pdf.gz | 940.7 KB | Display | |
Data in XML | 2wb1_validation.xml.gz | 239.1 KB | Display | |
Data in CIF | 2wb1_validation.cif.gz | 320 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/2wb1 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/2wb1 | HTTPS FTP |
-Related structure data
Related structure data | 2waqC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.99988, 0.0035, 0.01476), Vector: |
-Components
-DNA-DIRECTED RNA POLYMERASE ... , 12 types, 24 molecules AWBRCYETFUGVHZIKJQLMNOPX
#1: Protein | Mass: 99766.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB53*PLUS #2: Protein | Mass: 127582.016 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB54*PLUS #5: Protein | Mass: 20324.691 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB57*PLUS #6: Protein | Mass: 12822.612 Da / Num. of mol.: 2 / 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.: 2 / 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.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB61*PLUS #10: Protein | Mass: 12170.576 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB65*PLUS #11: Protein | Mass: 10211.846 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB62*PLUS #12: Protein | Mass: 7617.085 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB63*PLUS #13: Protein/peptide | Mass: 5606.951 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB64*PLUS |
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-Protein , 1 types, 2 molecules DS
#4: Protein | Mass: 30179.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) SULFOLOBUS SHIBATAE (archaea) / References: UniProt: B8YB56*PLUS |
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-Non-polymers , 3 types, 14 molecules
#14: Chemical | ChemComp-ZN / #15: Chemical | #16: Chemical | |
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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: 3.3 Å3/Da / Density % sol: 63.3 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 7MG/ML ENZYME, 150 MM KCL, 100MM SRCL2, 100MM CACODYLATE PH 6.5, 12% PEG MME 5K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.52→30.2 Å / Num. obs: 114084 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 3.52→3.62 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 62.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EN0 1en0 Resolution: 3.52→30.2 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.809 / SU B: 157.017 / SU ML: 1.068 / Cross valid method: THROUGHOUT / ESU R Free: 0.986 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE REFINEMENT FOR THIS ENTRY HAS NOT BEEN FINALIZED AND THEREFORE IT MUST BE CONSIDERED AS A WORK IN PROGRESS. SEE PDB ENTRY 2WAQ FOR ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE REFINEMENT FOR THIS ENTRY HAS NOT BEEN FINALIZED AND THEREFORE IT MUST BE CONSIDERED AS A WORK IN PROGRESS. SEE PDB ENTRY 2WAQ FOR FULLY REFINED MODEL. THE B FACTOR REFINEMENT HAS BEEN INITIALLY DONE BY DOMAIN IN CNS THEN OVERALL IN REFMAC. FOR MORE DETAILS SEE REFERENCE PAPER AND PDB ENTRY 2WAQ REFINED STRUCTURE
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.68 Å2
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Refinement step | Cycle: LAST / Resolution: 3.52→30.2 Å
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Refine LS restraints |
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