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- PDB-1dzf: RPB5 from S.cerevisiae -

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Basic information

Entry
Database: PDB / ID: 1dzf
TitleRPB5 from S.cerevisiae
ComponentsDNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1RNA polymerase
KeywordsTRANSFERASE / RNA POLYMERASE / RNA POLYMERASE SUBUNIT
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape ...RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / : / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / Formation of TC-NER Pre-Incision Complex / RNA polymerase II transcribes snRNA genes / RNA Polymerase I Promoter Escape / TP53 Regulates Transcription of DNA Repair Genes / Estrogen-dependent gene expression / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA-templated transcription / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / Dual incision in TC-NER / RNA polymerase I activity / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / transcription initiation at RNA polymerase I promoter / transcription elongation by RNA polymerase I / RNA polymerase I complex / transcription by RNA polymerase I / RNA polymerase III complex / transcription by RNA polymerase III / RNA polymerase II, core complex / transcription elongation by RNA polymerase II / transcription initiation at RNA polymerase II promoter / ribosome biogenesis / transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RPB5-like RNA polymerase subunit / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo5/Rpb5 ...Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1 / RNA polymerase, Rpb5, N-terminal domain / RPB5-like RNA polymerase subunit / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerases H / 23 Kd subunits signature. / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / RNA polymerase, subunit H/Rpb5 C-terminal / RPB5-like RNA polymerase subunit superfamily / RNA polymerase Rpb5, C-terminal domain / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC1
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsTodone, F. / Weinzierl, R.O.J. / Brick, P. / Onesti, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Crystal Structure of Rpb5, a Universal Eukaryotic RNA Polymerase Subunit and Trascription Factor Interaction Target
Authors: Todone, F. / Weinzierl, R.O.J. / Brick, P. / Onesti, S.
History
DepositionFeb 25, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1


Theoretical massNumber of molelcules
Total (without water)25,1171
Polymers25,1171
Non-polymers00
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.050, 82.220, 134.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2034-

HOH

21A-2121-

HOH

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1 / RNA polymerase / RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND ...RNA POLYMERASES I / II / AND III SUBUNIT ABC1 / ABC27 / DNA-DIRECTED RNA POLYMERASES I / II / AND III 27 KDA POLYPEPTIDE


Mass: 25117.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: S288C / Description: SYNTHETIC GENE / Cellular location: NUCLEAR / Gene: YBR154C OR YBR1204 / Plasmid: PGEX2TK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P20434, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 20% PEG 800, 200 MM AMMONIUM SA SULPHATE, 100 MM SODIUM CACODYLATE, PH 6.5
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
220-24 %PEG80001reservoir
315 %glycerol1reservoir
40.2 Mammonium sulfate1reservoir
50.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 19245 / % possible obs: 96.9 % / Redundancy: 4.7 % / Rsym value: 0.054 / Net I/σ(I): 8.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.226 / % possible all: 98.2
Reflection
*PLUS
Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 98.2 % / Rmerge(I) obs: 0.226

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→15 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.0001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.271 946 5 %RANDOM
Rwork0.217 ---
obs0.217 19230 98.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 0 169 1894
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.363
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.9011.5
X-RAY DIFFRACTIONx_mcangle_it3.012
X-RAY DIFFRACTIONx_scbond_it2.4152
X-RAY DIFFRACTIONx_scangle_it3.7612.5
LS refinement shellResolution: 1.9→1.99 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.4 135 6 %
Rwork0.32 2249 -
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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