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- PDB-5ui5: Crystal structure of Aquifex aeolicus sigmaN bound to promoter DNA -

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Basic information

Entry
Database: PDB / ID: 5ui5
TitleCrystal structure of Aquifex aeolicus sigmaN bound to promoter DNA
Components
  • DNA (30-MER)
  • DNA (31-MER)
  • RNA polymerase sigma factor RpoN
KeywordsTRANSCRIPTION/DNA / Helix-turn-helix DNA binding motif winged helix-turn-helix DNA binding motif bacterial RNA polymerase sigmaN bacterial RNA polymerase sigma54 / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


DNA-binding transcription activator activity / sigma factor activity / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / DNA binding
Similarity search - Function
RNA polymerase sigma-54 factor, core-binding domain / Sigma-54 factors family profile. / RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / RNA polymerase sigma factor 54 ...RNA polymerase sigma-54 factor, core-binding domain / Sigma-54 factors family profile. / RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / RNA polymerase sigma factor 54 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA polymerase sigma factor RpoN
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 3.4 Å
AuthorsDarst, S.A. / Campbell, E.A. / Rajashankar, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1 R35 GM118130 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Crystal structure of Aquifex aeolicus sigma (N) bound to promoter DNA and the structure of sigma (N)-holoenzyme.
Authors: Campbell, E.A. / Kamath, S. / Rajashankar, K.R. / Wu, M. / Darst, S.A.
History
DepositionJan 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (31-MER)
B: DNA (30-MER)
I: RNA polymerase sigma factor RpoN
N: DNA (31-MER)
O: DNA (30-MER)
V: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)118,8786
Polymers118,8786
Non-polymers00
Water57632
1
A: DNA (31-MER)
B: DNA (30-MER)
I: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)59,4393
Polymers59,4393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-27 kcal/mol
Surface area28730 Å2
MethodPISA
2
N: DNA (31-MER)
O: DNA (30-MER)
V: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)59,4393
Polymers59,4393
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-32 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.921, 99.921, 123.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: DNA chain DNA (31-MER)


Mass: 9626.262 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Aquifex aeolicus (bacteria)
#2: DNA chain DNA (30-MER)


Mass: 9474.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Aquifex aeolicus (bacteria)
#3: Protein RNA polymerase sigma factor RpoN


Mass: 40338.473 Da / Num. of mol.: 2 / Fragment: UNP residues 61-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (strain VF5) (bacteria)
Strain: VF5 / Gene: rpoN, aq_599 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O66858
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.99 Å3/Da / Density % sol: 58.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM sodium cacodylate, pH 6.5, 0.2 M KCl, 0.1 M Mg-acetate, 14%-18% Polyethylene glycol 8000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.987
SYNCHROTRONNSLS X3A20.987
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDAug 15, 2007
MAR CCD 165 mm2CCDDec 8, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9871
21
ReflectionResolution: 3.4→15 Å / Num. obs: 18717 / % possible obs: 99 % / Redundancy: 13.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 20.42
Reflection shellResolution: 3.4→3.52 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.903 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 3.4→14.99 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 41.72
RfactorNum. reflection% reflection
Rfree0.336 950 5.08 %
Rwork0.289 --
obs0.291 18697 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.4→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5258 2498 0 32 7788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048126
X-RAY DIFFRACTIONf_angle_d0.90711446
X-RAY DIFFRACTIONf_dihedral_angle_d24.9154550
X-RAY DIFFRACTIONf_chiral_restr0.091285
X-RAY DIFFRACTIONf_plane_restr0.0031029
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.57710.43361500.39372509X-RAY DIFFRACTION100
3.5771-3.79780.41511550.36452534X-RAY DIFFRACTION100
3.7978-4.08550.44311440.37712525X-RAY DIFFRACTION100
4.0855-4.48670.31971200.31742539X-RAY DIFFRACTION100
4.4867-5.11320.36721350.29932556X-RAY DIFFRACTION100
5.1132-6.35920.37521190.31732550X-RAY DIFFRACTION100
6.3592-14.99270.23971270.20822534X-RAY DIFFRACTION100

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