[English] 日本語
Yorodumi
- PDB-6pfj: Structure of S. venezuelae RsiG-WhiG-(ci-di-GMP) complex, P64 cry... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pfj
TitleStructure of S. venezuelae RsiG-WhiG-(ci-di-GMP) complex, P64 crystal form
Components
  • AmfC protein
  • RNA polymerase sigma factor
KeywordsTRANSCRIPTION / sigma / anti-sigma / c-di-GMP / developmental switch
Function / homology
Function and homology information


sigma factor activity / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA binding
Similarity search - Function
RNA polymerase sigma factor, FliA/WhiG / Sigma-70 factors family signature 1. / 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 ...RNA polymerase sigma factor, FliA/WhiG / Sigma-70 factors family signature 1. / 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
Similarity search - Domain/homology
Chem-C2E / RNA polymerase sigma factor / AmfC protein
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
Streptomyces sp. PanSC19 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.08 Å
AuthorsSchumacher, M.A.
CitationJournal: Mol.Cell / Year: 2020
Title: c-di-GMP Arms an Anti-sigma to Control Progression of Multicellular Differentiation in Streptomyces.
Authors: Gallagher, K.A. / Schumacher, M.A. / Bush, M.J. / Bibb, M.J. / Chandra, G. / Holmes, N.A. / Zeng, W. / Henderson, M. / Zhang, H. / Findlay, K.C. / Brennan, R.G. / Buttner, M.J.
History
DepositionJun 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 19, 2020Group: Database references / Structure summary / Category: chem_comp / citation
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.3Mar 13, 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: AmfC protein
A: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2974
Polymers50,9162
Non-polymers1,3812
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6940 Å2
ΔGint-17 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.089, 92.089, 96.646
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

-
Components

#1: Protein AmfC protein / RsiG


Mass: 19992.371 Da / Num. of mol.: 1 / Mutation: P91G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_3933 / Production host: Escherichia coli (E. coli) / References: UniProt: F2RFR7
#2: Protein RNA polymerase sigma factor / WhiG


Mass: 30924.023 Da / Num. of mol.: 1 / Mutation: D38E, S150T, T159S, E162D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. PanSC19 (bacteria) / Gene: EDD98_3685 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A3N1Q704
#3: Chemical ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate / Cyclic di-GMP


Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O14P2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris Bicine pH 8.5, 0.03 M sodium nitrate, 0.03 M sodium phosphate, 0.03 M ammonium sulfate, 9% MPD, 10% PEG 1000, 15% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→79.8 Å / Num. obs: 53003 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.5
Reflection shellResolution: 2.08→2.11 Å / Redundancy: 7 % / Rmerge(I) obs: 0.869 / Mean I/σ(I) obs: 1.4 / % possible all: 94

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACT3.25data extraction
AutoSolautosolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.08→79.75 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Phase error: 26.47
RfactorNum. reflection% reflection
Rfree0.238 3283 6.19 %
Rwork0.19 --
obs0.193 53003 96.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 75.09 Å2
Refinement stepCycle: LAST / Resolution: 2.08→79.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2897 0 92 43 3032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163046
X-RAY DIFFRACTIONf_angle_d1.2774142
X-RAY DIFFRACTIONf_dihedral_angle_d20.5971850
X-RAY DIFFRACTIONf_chiral_restr0.064478
X-RAY DIFFRACTIONf_plane_restr0.007524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.11110.36741130.31911717X-RAY DIFFRACTION77
2.1111-2.14410.37471180.32711787X-RAY DIFFRACTION79
2.1441-2.17920.39931150.36951866X-RAY DIFFRACTION83
2.1792-2.21680.31311320.28112006X-RAY DIFFRACTION89
2.2168-2.25710.32041390.26672116X-RAY DIFFRACTION94
2.2571-2.30050.29421590.25142224X-RAY DIFFRACTION99
2.3005-2.34750.26361380.21942192X-RAY DIFFRACTION100
2.3475-2.39850.22481480.21522219X-RAY DIFFRACTION100
2.3985-2.45430.251540.20232291X-RAY DIFFRACTION100
2.4543-2.51570.28091470.25052126X-RAY DIFFRACTION95
2.5157-2.58380.24871500.20922186X-RAY DIFFRACTION99
2.5838-2.65980.26281500.20042293X-RAY DIFFRACTION100
2.6598-2.74560.24821380.19312227X-RAY DIFFRACTION100
2.7456-2.84380.21981440.17792283X-RAY DIFFRACTION100
2.8438-2.95760.27531520.20722251X-RAY DIFFRACTION100
2.9576-3.09230.25581460.22632218X-RAY DIFFRACTION100
3.0923-3.25530.27091480.22112257X-RAY DIFFRACTION100
3.2553-3.45920.26391520.20132228X-RAY DIFFRACTION100
3.4592-3.72630.24851500.19212245X-RAY DIFFRACTION100
3.7263-4.10130.23921420.16372247X-RAY DIFFRACTION100
4.1013-4.69470.16851420.13872257X-RAY DIFFRACTION100
4.6947-5.91460.19331570.17122236X-RAY DIFFRACTION100
5.9146-79.81010.24141490.18322248X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -26.24 Å / Origin y: -3.0781 Å / Origin z: -0.2581 Å
111213212223313233
T0.3885 Å20.0854 Å20.0112 Å2-0.3899 Å20.0341 Å2--0.4322 Å2
L1.142 °21.5407 °2-0.5922 °2-4.0212 °2-0.6537 °2--1.7391 °2
S0.1924 Å °-0.1255 Å °-0.0025 Å °-0.2017 Å °-0.2849 Å °0.1199 Å °-0.0123 Å °0.0469 Å °-0.0261 Å °
Refinement TLS groupSelection details: ALL

+
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