[English] 日本語
Yorodumi
- PDB-6p8u: Structure of P. aeruginosa ATCC27853 CdnD:HORMA2:Peptide 1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p8u
TitleStructure of P. aeruginosa ATCC27853 CdnD:HORMA2:Peptide 1 complex
Components
  • HORMA domain containing protein
  • Nucleotidyltransferase
  • Peptide 1
KeywordsSIGNALING PROTEIN / second-messenger signaling / cGAS / CD-NTase / HORMA domain / closure motif
Function / homology
Function and homology information


diadenylate cyclase activity / diadenylate cyclase / nucleotide metabolic process / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / defense response to virus / ATP binding / metal ion binding
Similarity search - Function
Bacterial HORMA domain / Bacterial HORMA domain 2 / Second Messenger Oligonucleotide or Dinucleotide Synthetase domain / 2-5OAS/ClassI-CCAase, nucleotidyltransferase domain / HORMA domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Nucleotidyltransferase / CD-NTase-associated protein 7 / Cyclic AMP-AMP-AMP synthase / HORMA domain containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.893 Å
AuthorsYe, Q. / Corbett, K.D.
CitationJournal: Mol.Cell / Year: 2020
Title: HORMA Domain Proteins and a Trip13-like ATPase Regulate Bacterial cGAS-like Enzymes to Mediate Bacteriophage Immunity.
Authors: Ye, Q. / Lau, R.K. / Mathews, I.T. / Birkholz, E.A. / Watrous, J.D. / Azimi, C.S. / Pogliano, J. / Jain, M. / Corbett, K.D.
History
DepositionJun 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 4, 2020Group: Database references / Category: citation
Item: _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
A: Nucleotidyltransferase
B: HORMA domain containing protein
C: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9484
Polymers53,9243
Non-polymers241
Water5,531307
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.087, 43.373, 63.217
Angle α, β, γ (deg.)90.00, 104.18, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Nucleotidyltransferase / / Nucleotidyltransferase domain protein


Mass: 34063.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: DY979_07585, EGY23_20895, IPC669_24880, PA5486_02902, PAERUG_E15_London_28_01_14_04351, PAMH19_6112
Production host: Escherichia coli (E. coli) / References: UniProt: A0A080VY32, UniProt: P0DTF7*PLUS
#2: Protein HORMA domain containing protein


Mass: 18723.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: ORF C60, CAZ10_14260, DY940_15620, DY979_07580, EGY23_20890, EQH76_12140, IPC669_24875, PA5486_02901, PAERUG_E15_London_28_01_14_04350, PAMH19_6113
Production host: Escherichia coli (E. coli) / References: UniProt: Q8GQ50, UniProt: P0DTF6*PLUS
#3: Protein/peptide Peptide 1 /


Mass: 1137.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100 mM Bis-Tris pH 5.5, 0.2 M ammonium acetate, and 30% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.89→81.97 Å / Num. obs: 34946 / % possible obs: 97.7 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.086 / Rrim(I) all: 0.159 / Net I/σ(I): 7.1
Reflection shellResolution: 1.89→1.94 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.302 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1989 / CC1/2: 0.409 / Rpim(I) all: 0.837 / Rrim(I) all: 1.554 / % possible all: 87

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P82, 6P8R

6p82

6p8r


Resolution: 1.893→81.966 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 24.39
RfactorNum. reflection% reflection
Rfree0.2232 1704 4.89 %
Rwork0.1891 --
obs0.1907 34881 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.893→81.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 1 307 4070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053852
X-RAY DIFFRACTIONf_angle_d0.5865213
X-RAY DIFFRACTIONf_dihedral_angle_d11.5462285
X-RAY DIFFRACTIONf_chiral_restr0.041553
X-RAY DIFFRACTIONf_plane_restr0.003673
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8928-1.94850.34971310.32612482X-RAY DIFFRACTION88
1.9485-2.01140.31671430.28822770X-RAY DIFFRACTION99
2.0114-2.08330.33871440.2652785X-RAY DIFFRACTION98
2.0833-2.16670.28481350.24022763X-RAY DIFFRACTION98
2.1667-2.26530.2671530.222742X-RAY DIFFRACTION97
2.2653-2.38470.25381470.20262780X-RAY DIFFRACTION99
2.3847-2.53420.25331500.20752812X-RAY DIFFRACTION99
2.5342-2.72980.26011450.20492791X-RAY DIFFRACTION98
2.7298-3.00460.25121520.20392717X-RAY DIFFRACTION97
3.0046-3.43930.21891330.18932832X-RAY DIFFRACTION99
3.4393-4.33320.17561340.14612801X-RAY DIFFRACTION97
4.3332-82.0430.16161370.15352902X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.7730.0233-0.5360.42340.39451.7226-0.07990.114-0.0291-0.08560.02060.01220.0660.00760.05840.2226-0.0244-0.0190.19230.03520.2352-30.61936.128715.3436
21.9762-0.49590.5731.4445-0.08492.00610.0172-0.10420.07690.09710.0497-0.1547-0.1060.1556-0.0710.2296-0.02630.00120.2377-0.00020.2459-23.337324.830645.1354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B

+
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