[English] 日本語
Yorodumi
- PDB-1sig: CRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1sig
TitleCRYSTAL STRUCTURE OF A SIGMA70 SUBUNIT FRAGMENT FROM ESCHERICHIA COLI RNA POLYMERASE
ComponentsRNA POLYMERASE PRIMARY SIGMA FACTOR
KeywordsTRANSCRIPTION REGULATION / RNA POLYMERASE SIGMA FACTOR
Function / homology
Function and homology information


sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / response to heat / negative regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD ...RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor RpoD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MULTIWAVELENGTH ANOMALOUS DISPERSION / Resolution: 2.6 Å
AuthorsMalhotra, A. / Severinova, E. / Darst, S.A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1996
Title: Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase.
Authors: Malhotra, A. / Severinova, E. / Darst, S.A.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Domain Organization of the Escherichia Coli RNA Polymerase Sigma 70 Subunit
Authors: Severinova, E. / Severinov, K. / Fenyo, D. / Marr, M. / Brody, E.N. / Roberts, J.W. / Chait, B.T. / Darst, S.A.
History
DepositionFeb 18, 1997Processing site: BNL
Revision 1.0May 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA POLYMERASE PRIMARY SIGMA FACTOR


Theoretical massNumber of molelcules
Total (without water)39,0931
Polymers39,0931
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.229, 79.229, 134.060
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein RNA POLYMERASE PRIMARY SIGMA FACTOR / SIGMA70


Mass: 39092.883 Da / Num. of mol.: 1 / Fragment: RESIDUES 114 - 448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: RPOD / Plasmid: PET15B (NOVAGEN) / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Gene (production host): RPOD / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P00579
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growpH: 5.1
Details: PROTEIN CRYSTALLIZED FROM 50 MM SODIUM ACETATE, 0.5-0.7 M LI2SO4, 5-7% (W/V) PEG 8000, 5 MM DTT, PH 5.1; TRANSFERRED IN EIGHT STEPS TO 50 MM SODIUM ACETATE, 0.5 M LI2SO4, 15% (W/V) PEG 8000, ...Details: PROTEIN CRYSTALLIZED FROM 50 MM SODIUM ACETATE, 0.5-0.7 M LI2SO4, 5-7% (W/V) PEG 8000, 5 MM DTT, PH 5.1; TRANSFERRED IN EIGHT STEPS TO 50 MM SODIUM ACETATE, 0.5 M LI2SO4, 15% (W/V) PEG 8000, 17.5% GLYCEROL AND 10MM DTT, PH 5.1
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Severinova, E., (1996) J.Mol.Biol., 263, 637.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112.5-15 mg/mlprotein1drop
225 mMsodium acetate1drop
30.25-0.35 M1dropLi2SO4
42.5-3.5 %(w/v)PEG80001drop
52.5 mMDTT1drop
650 mMsodium acetate1reservoir
70.5-0.7 M1reservoirLi2SO4
85-7 %(w/v)PEG80001reservoir
95 mMDTT1reservoir

-
Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9663 / Wavelength: 0.9663, 0.9879
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Aug 25, 1995 / Details: COLLIMATOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96631
20.98791
ReflectionResolution: 2.6→15 Å / Num. obs: 13160 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 5.84 % / Biso Wilson estimate: 48.8 Å2 / Rsym value: 0.063 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 4.63 % / Mean I/σ(I) obs: 2.5 / Rsym value: 0.27 / % possible all: 78.3
Reflection
*PLUS
Num. measured all: 76887 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 78.3 % / Rmerge(I) obs: 0.27

-
Processing

Software
NameVersionClassification
MLPHAREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MULTIWAVELENGTH ANOMALOUS DISPERSION
Resolution: 2.6→6 Å / Rfactor Rfree error: 0.0092 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1170 10.28 %RANDOM
Rwork0.218 ---
obs0.218 11376 90.9 %-
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.1484 Å20 Å20 Å2
2---5.1484 Å20 Å2
3---10.2967 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.33 Å
Luzzati d res low-6 Å
Luzzati sigma a0.54 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.6→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 0 111 2593
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d21.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.411.5
X-RAY DIFFRACTIONx_mcangle_it5.332
X-RAY DIFFRACTIONx_scbond_it5.312
X-RAY DIFFRACTIONx_scangle_it7.952.5
LS refinement shellResolution: 2.6→2.71 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3707 133 10.84 %
Rwork0.3569 1094 -
obs--80.04 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg21.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46

+
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