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- PDB-1msw: Structural basis for the transition from initiation to elongation... -

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Basic information

Entry
Database: PDB / ID: 1msw
TitleStructural basis for the transition from initiation to elongation transcription in T7 RNA polymerase
Components
  • DNA-directed RNA polymerasePolymerase
  • Non-Template DNA
  • RNA message
  • Template DNA
KeywordsTRANSCRIPTION/DNA/RNA / T7RNAP elongation complex / TRANSCRIPTION-DNA-RNA COMPLEX
Function / homology
Function and homology information


DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal ...T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Helix Hairpins / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / T7 RNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsYin, Y.W. / Steitz, T.A.
CitationJournal: Science / Year: 2002
Title: Structural Basis for the Transition from Initiation to Elongation Transcription in T7 RNA Polymerase
Authors: Yin, Y.W. / Steitz, T.A.
History
DepositionSep 19, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
T: Template DNA
N: Non-Template DNA
R: RNA message
D: DNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)113,5364
Polymers113,5364
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.910, 145.460, 145.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Cell settingorthorhombic
Space group name H-MC2221

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Components

#1: DNA chain Template DNA


Mass: 6117.927 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Bacteriophage T7
#2: DNA chain Non-Template DNA


Mass: 5194.358 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Bacteriophage T7
#3: RNA chain RNA message


Mass: 3239.029 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in Bacteriophage T7
#4: Protein DNA-directed RNA polymerase / Polymerase / E.C.2.7.7.6 / T7 RNA polymerase / Bacteriophage T7 Rna Polymerase


Mass: 98984.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Plasmid: par1219 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00573, DNA-directed RNA polymerase
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.32 Å3/Da / Density % sol: 62.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, LiSO4, Mg(OAc)2, Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 294K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2LiSO411
3Mg(OAc)211
4Tris-HCLTris11
5PEG 800012
6LiSO412
7Mg(OAc)212
8Tris-HCLTris12
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMTris-HCl1reservoirpH7.0
2200 mM1reservoirLi2SO4
36 %PEG80001reservoir
410 mMmagnesium acetate1reservoir
55 mMdithiothreitol1reservoir
61
71
81

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.979
SYNCHROTRONNSLS X2521.05
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.051
ReflectionResolution: 2.1→20 Å / Num. all: 61181 / Num. obs: 61181 / % possible obs: 85 % / Biso Wilson estimate: 24.4 Å2
Reflection
*PLUS
Highest resolution: 2.1 Å / % possible obs: 89.2 % / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 55.4 %

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→20 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 4598334.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 4894 8 %RANDOM
Rwork0.241 ---
obs0.241 61181 85 %-
all-61181 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.6313 Å2 / ksol: 0.299966 e/Å3
Displacement parametersBiso mean: 76.1 Å2
Baniso -1Baniso -2Baniso -3
1--16.03 Å20 Å20 Å2
2--33 Å20 Å2
3----16.96 Å2
Refine analyzeLuzzati coordinate error free: 0.43 Å / Luzzati sigma a free: 0.77 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6802 964 0 190 7956
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.29
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it3.032.5
LS refinement shellResolution: 2.1→2.34 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.475 640 8 %
Rwork0.482 6996 -
obs--55.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 2 / Rfactor obs: 0.241 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.29
LS refinement shell
*PLUS
Rfactor Rfree: 0.475 / Rfactor Rwork: 0.482

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