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- PDB-1bdf: STRUCTURE OF ESCHERICHIA COLI RNA POLYMERASE ALPHA SUBUNIT N-TERM... -

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Basic information

Entry
Database: PDB / ID: 1bdf
TitleSTRUCTURE OF ESCHERICHIA COLI RNA POLYMERASE ALPHA SUBUNIT N-TERMINAL DOMAIN
ComponentsRNA POLYMERASE ALPHA SUBUNIT
KeywordsNUCLEOTIDYLTRANSFERASE / RNAP / ALPHA / ASSEMBLE
Function / homology
Function and homology information


submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination ...submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / protein dimerization activity / DNA binding / membrane / cytosol / cytoplasm
Similarity search - Function
DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / Beta Complex / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type ...DNA-directed RNA polymerase, insert domain / RNA polymerase, RBP11-like subunit / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Gyrase A; domain 2 / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / Beta Complex / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsZhang, G. / Darst, S.A.
CitationJournal: Science / Year: 1998
Title: Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain.
Authors: Zhang, G. / Darst, S.A.
History
DepositionMay 8, 1998Processing site: BNL
Revision 1.0May 11, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA POLYMERASE ALPHA SUBUNIT
B: RNA POLYMERASE ALPHA SUBUNIT
C: RNA POLYMERASE ALPHA SUBUNIT
D: RNA POLYMERASE ALPHA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)103,6544
Polymers103,6544
Non-polymers00
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.200, 117.200, 350.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
RNA POLYMERASE ALPHA SUBUNIT


Mass: 25913.492 Da / Num. of mol.: 4 / Fragment: N-TERMINAL DOMAIN RESIDUES 1-235 / Mutation: R45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cell line: BL-21 / Plasmid: PET15-B / Cell line (production host): BL-21 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 20

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.9 %
Crystal growpH: 8.75 / Details: pH 8.75
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
25 mMbeta-mercaptoethanol1reservoir
30.2 M1reservoirMgCl2
4100 mMTris-HCl1reservoir
5100 mM1reservoirNaCl
618-22 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97911
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 1, 1998 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 27865 / % possible obs: 86.9 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.06 / Rsym value: 0.057 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.19 / % possible all: 52.3
Reflection
*PLUS
Num. measured all: 145903

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→6 Å / Data cutoff high absF: 100000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.308 1178 5 %RANDOM
Rwork0.225 ---
obs0.225 23574 78.4 %-
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6939 0 0 257 7196
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_deg1.74
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it2.52
X-RAY DIFFRACTIONx_scangle_it2.52
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.5→2.6 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.36 70 5 %
Rwork0.28 1314 -
obs--40 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT

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