[English] 日本語
Yorodumi
- PDB-6p8s: Structure of P. aeruginosa ATCC27853 HORMA1:HORMA2:Peptide 1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p8s
TitleStructure of P. aeruginosa ATCC27853 HORMA1:HORMA2:Peptide 1 complex
Components
  • HORMA domain containing protein
  • HORMA1
  • Peptide 1
KeywordsPROTEIN BINDING / HORMA domain / closure motif / CD-NTase / cGAS
Function / homologyBacterial HORMA domain / Bacterial HORMA domain 2 / HORMA domain superfamily / defense response to virus / ACETATE ION / Type III CBASS phage resistance system CD-NTase-associated protein Cap8 / CD-NTase-associated protein 8 / CD-NTase-associated protein 7 / HORMA domain containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 7, 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: HORMA domain containing protein
B: HORMA domain containing protein
C: HORMA1
D: HORMA1
E: Peptide 1
F: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,00612
Polymers68,5436
Non-polymers4636
Water9,152508
1
A: HORMA domain containing protein
C: HORMA1
E: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6998
Polymers34,2713
Non-polymers4275
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-33 kcal/mol
Surface area13370 Å2
MethodPISA
2
B: HORMA domain containing protein
D: HORMA1
F: Peptide 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3074
Polymers34,2713
Non-polymers351
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-30 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.892, 124.539, 109.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-376-

HOH

21B-408-

HOH

31D-344-

HOH

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein HORMA domain containing protein


Mass: 18723.082 Da / Num. of mol.: 2
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
#2: Protein HORMA1


Mass: 14411.179 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: DY979_07575, EGY23_20885, IPC669_24870, PA5486_02900, PAERUG_E15_London_28_01_14_04349
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0F6RRN7, UniProt: P0DTF5*PLUS

-
Protein/peptide , 1 types, 2 molecules EF

#3: Protein/peptide Peptide 1


Mass: 1137.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli)

-
Non-polymers , 4 types, 514 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 0.5 M Sodium acetate, 31% PEG 3350, and 1 mM ATP

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→39.2 Å / Num. obs: 44741 / % possible obs: 96 % / Redundancy: 9.6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.074 / Rrim(I) all: 0.232 / Net I/σ(I): 8.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.878 / Mean I/σ(I) obs: 1 / Num. unique obs: 2481 / CC1/2: 0.521 / Rpim(I) all: 0.787 / Rrim(I) all: 2.043 / % possible all: 73.7

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P8P, 6P8R

6p8p

6p8r


Resolution: 2→39.197 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.6
RfactorNum. reflection% reflection
Rfree0.2272 2292 5.13 %
Rwork0.1912 --
obs0.1931 44644 95.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→39.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 27 508 5238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064825
X-RAY DIFFRACTIONf_angle_d0.7466542
X-RAY DIFFRACTIONf_dihedral_angle_d11.9392860
X-RAY DIFFRACTIONf_chiral_restr0.045723
X-RAY DIFFRACTIONf_plane_restr0.005836
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.04360.3958990.33721951X-RAY DIFFRACTION71
2.0436-2.09110.29561210.30712166X-RAY DIFFRACTION79
2.0911-2.14340.31841180.2712411X-RAY DIFFRACTION88
2.1434-2.20130.28881470.25452611X-RAY DIFFRACTION96
2.2013-2.26610.29281250.23082752X-RAY DIFFRACTION100
2.2661-2.33920.24941620.21562745X-RAY DIFFRACTION100
2.3392-2.42280.28831490.21062753X-RAY DIFFRACTION100
2.4228-2.51980.24481570.21482720X-RAY DIFFRACTION100
2.5198-2.63450.28411400.20352716X-RAY DIFFRACTION99
2.6345-2.77330.24271490.20652779X-RAY DIFFRACTION100
2.7733-2.9470.20861500.19562746X-RAY DIFFRACTION100
2.947-3.17450.21881540.19092738X-RAY DIFFRACTION99
3.1745-3.49380.21091480.16892777X-RAY DIFFRACTION100
3.4938-3.99890.18971410.15372789X-RAY DIFFRACTION99
3.9989-5.03650.18291630.1352805X-RAY DIFFRACTION100
5.0365-39.20490.19841690.18482893X-RAY DIFFRACTION99
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)
11.70550.44840.35232.9709-0.79591.3755-0.0014-0.0429-0.08570.03360.03390.0030.1290.0173-0.01970.20580.03730.02580.1572-0.02040.171218.294925.589416.1722
22.13561.5254-0.50752.899-0.522.1048-0.12620.1367-0.0089-0.29590.02590.02770.1997-0.13270.07830.24390.00940.00020.1533-0.00420.131122.6782-9.036612.4601
33.7323-0.2440.45493.7336-1.04452.1610.03970.2758-0.004-0.1271-0.020.1395-0.0874-0.0286-0.01060.20430.03140.01920.1672-0.01790.14435.635240.5683-0.4886
41.51220.77211.04411.54760.3973.6117-0.0276-0.05070.1225-0.0594-0.0380.0348-0.2960.06090.08190.19210.02490.01650.1448-0.01810.131929.307-1.439236.2135
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A or chain E
2X-RAY DIFFRACTION2Chain B or chain F
3X-RAY DIFFRACTION3Chain C
4X-RAY DIFFRACTION4Chain D

+
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