[English] 日本語
Yorodumi
- PDB-1cez: CRYSTAL STRUCTURE OF A T7 RNA POLYMERASE-T7 PROMOTER COMPLEX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cez
TitleCRYSTAL STRUCTURE OF A T7 RNA POLYMERASE-T7 PROMOTER COMPLEX
Components
  • DNA (5'-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3')
  • DNA (5'-D(P*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3')
  • PROTEIN (BACTERIOPHAGE T7 RNA POLYMERASE)
KeywordsTRANSFERASE/DNA / T7 RNA POLYMERASE / 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 / MIRAS / Resolution: 2.4 Å
AuthorsCheetham, G.M.T. / Jeruzalmi, D. / Steitz, T.A.
CitationJournal: Nature / Year: 1999
Title: Structural basis for initiation of transcription from an RNA polymerase-promoter complex.
Authors: Cheetham, G.M. / Jeruzalmi, D. / Steitz, T.A.
History
DepositionMar 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0May 21, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: 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: DNA (5'-D(P*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3')
N: DNA (5'-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3')
A: PROTEIN (BACTERIOPHAGE T7 RNA POLYMERASE)


Theoretical massNumber of molelcules
Total (without water)108,7783
Polymers108,7783
Non-polymers00
Water8,485471
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)220.100, 73.300, 80.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

-
Components

#1: DNA chain DNA (5'-D(P*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP*AP*TP*TP*A)-3') / PROMOTER TEMPLATE STRAND


Mass: 5256.431 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3') / PROMOTER NON-TEMPLATE STRAND


Mass: 4536.987 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein PROTEIN (BACTERIOPHAGE T7 RNA POLYMERASE) / EC 2.7.7.6


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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00573, DNA-directed RNA polymerase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 58 %
Crystal growpH: 8.7 / Details: pH 8.7
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein1drop
220 %PEG80001reservoir
3200 mMammonium sulfate1reservoir
40.25 %beta-n-octylglucopyranoside1reservoir
5100 mMTris-HCl1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91
DetectorType: ADSC / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 50077 / % possible obs: 96.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 48.6 Å2 / Rsym value: 0.084 / Net I/σ(I): 11.9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.9 / Rsym value: 0.39 / % possible all: 97.3
Reflection
*PLUS
Rmerge(I) obs: 0.08

-
Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.5refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→40 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.27 4243 10 %RANDOM
Rwork0.224 ---
obs0.224 42312 81.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 53.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.91 Å20 Å20 Å2
2--1.2 Å20 Å2
3----8.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6639 656 0 471 7766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.112
X-RAY DIFFRACTIONc_scbond_it3.12
X-RAY DIFFRACTIONc_scangle_it4.392.5
LS refinement shellResolution: 2.4→2.47 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.341 187 8.6 %
Rwork0.302 1984 -
obs--50.5 %
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
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg20.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it3.12
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor obs: 0.32

+
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