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- PDB-3gfk: Crystal structure of Bacillus subtilis Spx/RNA polymerase alpha s... -

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Basic information

Entry
Database: PDB / ID: 3gfk
TitleCrystal structure of Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex
Components
  • DNA-directed RNA polymerase subunit alphaPolymerase
  • Regulatory protein spx
KeywordsTranscription/Transferase / protein-protein complex / Cytoplasm / Redox-active center / Stress response / Transcription / Transcription regulation / DNA-directed RNA polymerase / Nucleotidyltransferase / Transferase / Transcription-Transferase COMPLEX
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / protein dimerization activity / negative regulation of DNA-templated transcription / DNA-templated transcription / DNA binding / cytoplasm
Similarity search - Function
Global transcriptional regulator Spx / Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / DNA-directed RNA polymerase, insert domain ...Global transcriptional regulator Spx / Transcriptional regulator Spx/MgsR / Arsenate reductase-like / ArsC family / ArsC family profile. / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / 5' to 3' exonuclease, C-terminal subdomain / 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 / Glutaredoxin / Glutaredoxin / DNA polymerase; domain 1 / Thioredoxin-like superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Global transcriptional regulator Spx / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLamour, V. / Westblade, L.F. / Campbell, E.A. / Darst, S.A.
CitationJournal: J.Struct.Biol. / Year: 2009
Title: Crystal structure of the in vivo-assembled Bacillus subtilis Spx/RNA polymerase alpha subunit C-terminal domain complex
Authors: Lamour, V. / Westblade, L.F. / Campbell, E.A. / Darst, S.A.
History
DepositionFeb 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regulatory protein spx
B: DNA-directed RNA polymerase subunit alpha


Theoretical massNumber of molelcules
Total (without water)24,6702
Polymers24,6702
Non-polymers00
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-5 kcal/mol
Surface area11890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.900, 44.300, 117.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Regulatory protein spx


Mass: 15551.892 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: spxA, BSU11500 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O31602
#2: Protein DNA-directed RNA polymerase subunit alpha / Polymerase / RNAP subunit alpha / Transcriptase subunit alpha / RNA polymerase subunit alpha


Mass: 9118.472 Da / Num. of mol.: 1 / Fragment: Alpha C-terminal domain (alpha-CTD)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rpoA, BSU01430 / Production host: Escherichia coli (E. coli) / References: UniProt: P20429, DNA-directed RNA polymerase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5
Details: vapor diffusion against 6% (w/v) PEG 6000, 100 mM sodium acetate, pH 5.0, 10 micromolar CuCl2, protein concentration 11.5 mg/mL, temperature 295K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.3376
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3376 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. obs: 11313 / % possible obs: 99.4 %

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Processing

Software
NameClassification
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z3E

1z3e


Resolution: 2.3→20 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.282 523 -RANDOM
Rwork0.229 ---
obs0.229 10088 98.9 %-
all-10201 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.211 Å20 Å20 Å2
2--1.818 Å20 Å2
3----1.607 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1586 0 0 257 1843
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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