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- PDB-3ihq: Crystal Structure of Reduced C10S Spx in Complex with the Alpha C... -

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Basic information

Entry
Database: PDB / ID: 3ihq
TitleCrystal Structure of Reduced C10S Spx in Complex with the Alpha C-terminal Domain of RNA Polymeras
Components
  • DNA-directed RNA polymerase subunit alphaPolymerase
  • Regulatory protein spx
KeywordsTranscription/Transferase / transcription regulation / oxidative stress / Spx / RNA Polymerase / Cytoplasm / Disulfide bond / Redox-active center / Stress response / Transcription / 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
IMIDAZOLE / Global transcriptional regulator Spx / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNewberry, K.J. / Brennan, R.G.
Citation
Journal: Plos One / Year: 2010
Title: Promoter recognition by a complex of Spx and the C-terminal domain of the RNA polymerase alpha subunit.
Authors: Nakano, M.M. / Lin, A. / Zuber, C.S. / Newberry, K.J. / Brennan, R.G. / Zuber, P.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Crystal structure of the Bacillus subtilis anti-alpha, global transcriptional regulator, Spx, in complex with the {alpha} C-terminal domain of RNA polymerase
Authors: Newberry, K.J. / Nakano, S. / Zuber, P. / Brennan, R.G.
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)24,2783
Polymers24,2092
Non-polymers691
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-5 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.390, 32.220, 50.580
Angle α, β, γ (deg.)106.07, 91.62, 103.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Regulatory protein spx


Mass: 15673.976 Da / Num. of mol.: 1 / Mutation: C10S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU11500, spxA / Plasmid: pPROEX / 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: 8534.862 Da / Num. of mol.: 1 / Fragment: UNP residues 245-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU01430, rpoA / Plasmid: PET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (BL21) / References: UniProt: P20429, DNA-directed RNA polymerase
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.85 Å3/Da / Density % sol: 33.47 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 25-30% PEG 4000, 0.1 M sodium citrate, 0.1 M magnesium chloride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2006 / Details: Double Crystal Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.33 Å / Num. obs: 12912 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Net I/σ(I): 7.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.9 / Num. unique all: 12912 / Rsym value: 0.23 / % possible all: 94.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z3E

1z3e


Resolution: 1.9→48.33 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2784 662 -random
Rwork0.2364 ---
all-13584 --
obs-12912 95.1 %-
Displacement parametersBiso mean: 38.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→48.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 5 39 1520
LS refinement shellResolution: 1.9→1.97 Å
RfactorNum. reflection
Rfree0.405 70
Rwork0.3109 -
obs-1223

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