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- PDB-3c3l: X-ray crystal structure of the N4 mini-vRNAP P2 promoter complex -

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Basic information

Entry
Database: PDB / ID: 3c3l
TitleX-ray crystal structure of the N4 mini-vRNAP P2 promoter complex
Components
  • P2 Promoter DNA
  • Virion RNA polymerase
Keywordstransferase/DNA / protein-DNA complex / nucleotidyltransferase / promoter binary complex / DNA-hairpin / virion RNA polymerase / transferase-DNA COMPLEX
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / virion component / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / GTP binding / ATP binding / metal ion binding
Similarity search - Function
Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #110 / Alpha-Beta Plaits - #2440 / Transcription Regulator spoIIAA - #220 / Helix Hairpins - #1360 / Helix Hairpins - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1860 / : / : / Virion DNA-directed RNA polymerase, plug insertion / Virion DNA-directed RNA polymerase domain ...Butyryl-CoA Dehydrogenase, subunit A; domain 3 - #110 / Alpha-Beta Plaits - #2440 / Transcription Regulator spoIIAA - #220 / Helix Hairpins - #1360 / Helix Hairpins - #1370 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1860 / : / : / Virion DNA-directed RNA polymerase, plug insertion / Virion DNA-directed RNA polymerase domain / Transcription Regulator spoIIAA / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Helix Hairpins / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Alpha-Beta Plaits / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesBacteriophage N4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsGleghorn, M.L. / Murakami, K.S.
CitationJournal: Mol.Cell / Year: 2008
Title: Structural basis for DNA-hairpin promoter recognition by the bacteriophage N4 virion RNA polymerase.
Authors: Gleghorn, M.L. / Davydova, E.K. / Rothman-Denes, L.B. / Murakami, K.S.
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: P2 Promoter DNA
D: P2 Promoter DNA
A: Virion RNA polymerase
B: Virion RNA polymerase


Theoretical massNumber of molelcules
Total (without water)266,3724
Polymers266,3724
Non-polymers00
Water5,242291
1
C: P2 Promoter DNA
A: Virion RNA polymerase


Theoretical massNumber of molelcules
Total (without water)133,1862
Polymers133,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-7.1 kcal/mol
Surface area46120 Å2
MethodPISA
2
D: P2 Promoter DNA
B: Virion RNA polymerase


Theoretical massNumber of molelcules
Total (without water)133,1862
Polymers133,1862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-6.1 kcal/mol
Surface area45830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.344, 111.205, 276.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: DNA chain P2 Promoter DNA


Mass: 10149.539 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein Virion RNA polymerase


Mass: 123036.320 Da / Num. of mol.: 2 / Fragment: residues 998-2102
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage N4 (virus) / Gene: vRNAP / Plasmid: pKMK56 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q859P9, DNA-directed RNA polymerase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 0.3 M dibasic ammonium citrate, 25 % (drop) or 15% (reservoir) PEG 3350, hanging drop, temperature 294K, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HClTris11
2dibasic ammonium citrate11
3PEG 335011
4Tris-HClTris12
5dibasic ammonium citrate12
6PEG 335012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5414 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 16, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 92251 / % possible obs: 93.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Χ2: 1.092 / Net I/σ(I): 27.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.493.30.18482141.18183.7
2.49-2.593.30.16989201.14391.5
2.59-2.73.30.14592021.11393.9
2.7-2.853.30.12493511.11795.4
2.85-3.023.50.10694911.18996.6
3.02-3.263.90.08895011.02696.3
3.26-3.584.30.07194461.08195.5
3.58-4.14.60.05894061.13994.5
4.1-5.164.90.04793491.04893.5
5.16-304.90.03293710.98590.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 2.4→30 Å / FOM work R set: 0.866 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.246 9037 9 %
Rwork0.215 --
obs-90497 90.3 %
Solvent computationBsol: 19.391 Å2
Displacement parametersBiso mean: 26.38 Å2
Baniso -1Baniso -2Baniso -3
1-6.49 Å20 Å20 Å2
2---4.18 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16768 780 0 291 17839
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.238
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water.param

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