[English] 日本語
Yorodumi
- PDB-2pi5: T7 RNA polymerase complexed with a phi10 promoter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pi5
TitleT7 RNA polymerase complexed with a phi10 promoter
Components
  • 5'-D(*CP*TP*TP*C*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3'
  • 5'-D(*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*T)-3'
  • DNA-directed RNA polymerasePolymerase
KeywordsTransferase/DNA / T7 RNA polymerase / initiating nucleoites / Transferase-DNA 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) / T7 RNA polymerase
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKennedy, W.P. / Momand, J.R. / Yin, Y.W.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Mechanism for de novo RNA synthesis and initiating nucleotide specificity by t7 RNA polymerase.
Authors: Kennedy, W.P. / Momand, J.R. / Yin, Y.W.
History
DepositionApr 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
T: 5'-D(*CP*TP*TP*C*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3'
P: 5'-D(*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*T)-3'
A: DNA-directed RNA polymerase


Theoretical massNumber of molelcules
Total (without water)109,3673
Polymers109,3673
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.450, 73.791, 80.315
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: DNA chain 5'-D(*CP*TP*TP*C*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3'


Mass: 6732.362 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*T)-3'


Mass: 4223.780 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA-directed RNA polymerase / Polymerase


Mass: 98410.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Production host: Escherichia coli (E. coli) / References: UniProt: P00573, DNA-directed RNA polymerase

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Tris-HCl, 200 mM Li2SO4, 20% PEG 8000, 5% Glycerol, 15 mM magnesium acetate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tris-HClTris11
2Li2SO411
3PEG 800011
4Glycerol11
5magnesium acetate11
6Tris-HClTris12
7Li2SO412
8PEG 800012
9Glycerol12
10magnesium acetate12

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 29104 / Num. obs: 29104 / % possible obs: 96.6 % / Observed criterion σ(F): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 48.1 Å2 / Rsym value: 0.134 / Net I/σ(I): 1.8

-
Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→39.04 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 310854.16 / Data cutoff high rms absF: 310854.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1233 4.5 %RANDOM
Rwork0.249 ---
obs0.249 27222 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5264 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 84.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.13 Å20 Å20 Å2
2---7.12 Å20 Å2
3---2.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 2.9→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6803 648 0 0 7451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
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_d1.04
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 69 2 %
Rwork0.401 3395 -
obs--69.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna.paramdna-rna.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water.paramwater.top

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more