[English] 日本語
Yorodumi
- PDB-6pfv: Structure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhomb... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pfv
TitleStructure of S. venezuelae RisG-WhiG-c-di-GMP complex: orthorhombic crystal form
Components
  • AmfC protein
  • RNA polymerase sigma factor
KeywordsTRANSCRIPTION / RsiG / WhiG / c-di-GMP / sigma / anti-sigma / Streptomyces
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 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 22, 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 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
B: AmfC protein
D: RNA polymerase sigma factor
E: AmfC protein
G: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,54912
Polymers152,4076
Non-polymers4,1426
Water0
1
T: AmfC protein
A: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1834
Polymers50,8022
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6890 Å2
ΔGint-20 kcal/mol
Surface area18740 Å2
MethodPISA
2
B: AmfC protein
D: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1834
Polymers50,8022
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-20 kcal/mol
Surface area17990 Å2
MethodPISA
3
E: AmfC protein
G: RNA polymerase sigma factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1834
Polymers50,8022
Non-polymers1,3812
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-23 kcal/mol
Surface area18540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.847, 97.339, 204.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein AmfC protein / RsiG


Mass: 19992.371 Da / Num. of mol.: 3 / 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: 30809.855 Da / Num. of mol.: 3 / Mutation: D38E, I97V, R144G, 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.: 6 / Source method: obtained synthetically / Formula: C20H24N10O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.74 %
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 and 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: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.99→87.897 Å / Num. obs: 59828 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.053 / Net I/σ(I): 8.9
Reflection shellResolution: 2.99→3.04 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2129 / CC1/2: 0.447 / Rpim(I) all: 0.653 / % possible all: 99.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PFJ

6pfj


Resolution: 3→87.897 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0.23 / Phase error: 33.04
RfactorNum. reflection% reflection
Rfree0.2784 3613 6.04 %
Rwork0.2139 --
obs0.2178 59828 97.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 256.36 Å2 / Biso mean: 112.7061 Å2 / Biso min: 32.82 Å2
Refinement stepCycle: final / Resolution: 3→87.897 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9026 0 276 0 9302
Biso mean--76.67 --
Num. residues----1146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079458
X-RAY DIFFRACTIONf_angle_d0.97512864
X-RAY DIFFRACTIONf_chiral_restr0.0511486
X-RAY DIFFRACTIONf_plane_restr0.0051632
X-RAY DIFFRACTIONf_dihedral_angle_d21.1885761
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.03950.47251350.37482129226496
3.0395-3.08110.32191420.34062181232397
3.0811-3.12510.42631420.33332157229997
3.1251-3.17180.37851390.34382149228897
3.1718-3.22140.39411440.35362190233498
3.2214-3.27420.37491320.33022131226397
3.2742-3.33060.41631440.33142228237297
3.3306-3.39120.42011410.31712142228398
3.3912-3.45640.41111340.28622165229996
3.4564-3.5270.33521390.2722058219793
3.527-3.60370.36661360.25922159229596
3.6037-3.68750.38431420.25492151229398
3.6875-3.77970.32551370.22892176231398
3.7797-3.88190.31691360.23072189232598
3.8819-3.99610.291340.22062184231897
3.9961-4.12510.27081380.19342122226097
4.1251-4.27260.28151360.18792164230097
4.2726-4.44360.22741400.16832165230596
4.4436-4.64580.20511430.1622200234399
4.6458-4.89080.21891390.16892176231598
4.8908-5.19720.26621430.17142151229498
5.1972-5.59840.27951370.19592159229697
5.5984-6.16160.23651460.20042178232497
6.1616-7.05290.27581390.21152194233398
7.0529-8.88460.19791380.16122162230096
8.8846-87.93460.22221370.18592155229297
Refinement TLS params.Method: refined / Origin x: 54.1987 Å / Origin y: 32.2717 Å / Origin z: 15.9632 Å
111213212223313233
T0.2005 Å2-0.0381 Å20.003 Å2-0.181 Å2-0.3193 Å2--0.1653 Å2
L0.043 °20.0081 °20.0827 °2--0.0139 °20.0778 °2--0.0671 °2
S0.18 Å °0.0086 Å °0.0186 Å °0.0966 Å °-0.0315 Å °0.054 Å °0.0627 Å °0.0715 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allT36 - 199
2X-RAY DIFFRACTION1allR203 - 201
3X-RAY DIFFRACTION1allA24 - 275
4X-RAY DIFFRACTION1allB40 - 199
5X-RAY DIFFRACTION1allC203 - 201
6X-RAY DIFFRACTION1allD24 - 275
7X-RAY DIFFRACTION1allE41 - 199
8X-RAY DIFFRACTION1allF203 - 201
9X-RAY DIFFRACTION1allG21 - 275

+
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