[English] 日本語
Yorodumi
- PDB-1aro: T7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aro
TitleT7 RNA POLYMERASE COMPLEXED WITH T7 LYSOZYME
Components
  • T7 LYSOZYME
  • T7 RNA POLYMERASE
KeywordsCOMPLEX (POLYMERASE/HYDROLASE) / TRANSCRIPTION / DNA-DIRECTED RNA POLYMERASE / HYDROLASE / GLYCOSIDASE / COMPLEX (POLYMERASE-HYDROLASE) / COMPLEX (POLYMERASE-HYDROLASE) complex
Function / homology
Function and homology information


DNA-templated viral transcription / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / negative regulation of viral transcription / viral release from host cell by cytolysis / peptidoglycan catabolic process / DNA-directed RNA polymerase complex / : / : / : ...DNA-templated viral transcription / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase activity / negative regulation of viral transcription / viral release from host cell by cytolysis / peptidoglycan catabolic process / DNA-directed RNA polymerase complex / : / : / : / : / : / : / DNA-directed RNA polymerase / host cell cytoplasm / defense response to bacterium / DNA binding / zinc ion binding
Similarity search - Function
Endolysin T7 type / Helix Hairpins - #260 / Helix Hairpins - #280 / T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / 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. ...Endolysin T7 type / Helix Hairpins - #260 / Helix Hairpins - #280 / T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / 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. / Peptidoglycan recognition protein family domain, metazoa/bacteria / Peptidoglycan recognition protein / Animal peptidoglycan recognition proteins homologous to Bacteriophage T3 lysozyme. / Lysozyme-like / Peptidoglycan recognition protein-like / Ami_2 / N-acetylmuramoyl-L-alanine amidase / N-acetylmuramoyl-L-alanine amidase domain / N-acetylmuramoyl-L-alanine amidase/PGRP domain superfamily / 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 / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / T7 RNA polymerase / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsSteitz, T. / Jeruzalmi, D.
CitationJournal: EMBO J. / Year: 1998
Title: Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme.
Authors: Jeruzalmi, D. / Steitz, T.A.
History
DepositionAug 8, 1997Processing site: BNL
Revision 1.0Oct 21, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: T7 RNA POLYMERASE
L: T7 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,3479
Polymers115,9432
Non-polymers1,4047
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)273.385, 95.612, 63.582
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein T7 RNA POLYMERASE


Mass: 98936.039 Da / Num. of mol.: 1 / Mutation: C347S, C723S, C839S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: T7 / Plasmid: T7 / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00573, DNA-directed RNA polymerase
#2: Protein T7 LYSOZYME / N-ACETYLMURAMOYL-L-ALANINE AMIDASE


Mass: 17007.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Genus: T7-like viruses / Gene: T7 / Plasmid: T7 / Species (production host): Escherichia coli / Gene (production host): T7 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P00806, N-acetylmuramoyl-L-alanine amidase
#3: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Hg

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 69 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 12 ℃ / Method: vapor diffusion, sitting drop / Details: Jeruzalmi, D., (1997) J. Mol. Biol., 274, 748.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 mg/mlprotein1drop
22.5 mMTris-HCl1drop
35 mMpotassium phosphate1drop
460 mM1dropNaCl
525 mM1dropMgCl2
612-15 %sarcosine1drop
71 mMdithiothreitol1drop
81 mMNa3 EDTA1drop
90.05 %(v/v)beta-hexylglucoside1drop
100.02 %1dropNaN3
11water1reservoirdeionized, 0.500ml

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.908
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Oct 1, 1993 / Details: MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 38310 / % possible obs: 93.9 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 13.37
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2 / Rsym value: 0.44 / % possible all: 76.8

-
Processing

Software
NameClassification
CNSrefinement
DEMON-ANGELmodel building
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
DEMON-ANGELphasing
X-PLORphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.309 --
Rwork0.262 --
obs0.262 38310 93.9 %
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7599 0 6 0 7605
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.8

+
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