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- PDB-3c46: X-ray crystal structure of the N4 mini-vRNAP P2_7a promoter compl... -

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Basic information

Entry
Database: PDB / ID: 3c46
TitleX-ray crystal structure of the N4 mini-vRNAP P2_7a promoter complex soaked with MgCl2
Components
  • P2_7a Promoter DNA
  • Virion RNA polymerase
Keywordstransferase/DNA / protein-DNA complex / nucleotidyltransferase / promoter binary complex / DNA-hairpin / virion RNA polymerase / phosphate ion / 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
DIHYDROGENPHOSPHATE ION / DNA / DNA (> 10) / Virion DNA-directed RNA polymerase
Similarity search - Component
Biological speciesBacteriophage N4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 29, 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
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
A: Virion RNA polymerase
C: P2_7a Promoter DNA
B: Virion RNA polymerase
D: P2_7a Promoter DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,2816
Polymers268,0874
Non-polymers1942
Water17,421967
1
A: Virion RNA polymerase
C: P2_7a Promoter DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1403
Polymers134,0432
Non-polymers971
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-1.4 kcal/mol
Surface area46380 Å2
MethodPISA
2
B: Virion RNA polymerase
D: P2_7a Promoter DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1403
Polymers134,0432
Non-polymers971
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-4.7 kcal/mol
Surface area46670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.622, 111.424, 276.763
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 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
#2: DNA chain P2_7a Promoter DNA


Mass: 11007.082 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 0.21 M dibasic ammonium citrate, 0.09 M ammonium dihydrogen monophosphate, 25 % (drop) or 15% (reservoir) PEG 3350, hanging drop, temperature 294K, VAPOR DIFFUSION, HANGING DROP
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HCl11
2dibasic ammonium citrate11
3ammonium dihydrogen monophosphate11
4PEG 335011
5Tris-HCl12
6dibasic ammonium citrate12
7ammonium dihydrogen monophosphate12
8PEG 335012

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC Q315 / Detector: CCD / Date: Jul 30, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 148149 / % possible obs: 85.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.081 / Χ2: 1.047 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.0730.472130070.96475.9
2.07-2.1530.349131810.99277.1
2.15-2.2530.261132011.0876.9
2.25-2.3730.2134361.15978
2.37-2.522.90.149135201.15678.7
2.52-2.712.90.118145171.14284.2
2.71-2.992.80.09160651.03693
2.99-3.422.90.066169391.12597.6
3.42-4.3130.055170900.83397.6
4.31-503.20.045171931.03995.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 2→50 Å / FOM work R set: 0.841 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.242 14185 8.2 %
Rwork0.21 --
obs-142302 82.3 %
Solvent computationBsol: 30.24 Å2
Displacement parametersBiso mean: 28.881 Å2
Baniso -1Baniso -2Baniso -3
1-4.635 Å20 Å20 Å2
2---2.43 Å20 Å2
3----2.206 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16897 822 10 967 18696
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3111.5
X-RAY DIFFRACTIONc_scbond_it2.1562
X-RAY DIFFRACTIONc_mcangle_it2.0322
X-RAY DIFFRACTIONc_scangle_it3.2212.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION32hp_xplor_par.txt
X-RAY DIFFRACTION4CNS_TOPPAR:water.param

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