[English] 日本語
Yorodumi
- PDB-6p8o: Structure of P. aeruginosa ATCC27853 HORMA2-deltaC -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6p8o
TitleStructure of P. aeruginosa ATCC27853 HORMA2-deltaC
Components(HORMA domain containing protein) x 2
KeywordsPROTEIN BINDING / HORMA domain / CD-NTase
Function / homologyBacterial HORMA domain / Bacterial HORMA domain 2 / HORMA domain superfamily / defense response to virus / NICKEL (II) ION / CD-NTase-associated protein 7 / HORMA domain containing protein
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.604 Å
AuthorsYe, Q. / Corbett, K.D. / Lau, R.K.
Citation
Journal: 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.
#1: Journal: Mol.Cell / Year: 2020
Title: Structure and mechanism of a cyclic trinucleotide-activated bacterial endonuclease mediating bacteriophage immunity
Authors: Lau, R.K. / Ye, Q. / Birkholz, E.A. / Berg, K.R. / Patel, L. / Mathews, I.T. / Watrous, J.D. / Ego, K. / Whiteley, A.T. / Lowey, B. / Mekalanos, J.J. / Kranzusch, P.J. / Jain, M. / Pogliano, J. / 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 / citation_author
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.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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HORMA domain containing protein
B: HORMA domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4794
Polymers30,3842
Non-polymers942
Water3,621201
1
A: HORMA domain containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3133
Polymers15,2191
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HORMA domain containing protein


Theoretical massNumber of molelcules
Total (without water)15,1651
Polymers15,1651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.421, 30.585, 74.911
Angle α, β, γ (deg.)90.00, 101.57, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HORMA domain containing protein


Mass: 15219.276 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
#2: Protein HORMA domain containing protein


Mass: 15165.185 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: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.42 Å3/Da / Density % sol: 49.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 10 mM NiCl2, and 20% PEG 2000 MME.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 38122 / % possible obs: 98.5 % / Redundancy: 3.1 % / CC1/2: 0.992 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Net I/σ(I): 18.4
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 1759 / CC1/2: 0.746 / Rpim(I) all: 0.33 / Rrim(I) all: 0.581 / % possible all: 92.2

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P8R

6p8r


Resolution: 1.604→44.094 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.31
RfactorNum. reflection% reflection
Rfree0.2077 1852 4.86 %
Rwork0.191 --
obs0.1919 38104 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.604→44.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 2 201 2287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052137
X-RAY DIFFRACTIONf_angle_d0.7122910
X-RAY DIFFRACTIONf_dihedral_angle_d11.1981246
X-RAY DIFFRACTIONf_chiral_restr0.048326
X-RAY DIFFRACTIONf_plane_restr0.004354
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6037-1.64710.26261240.23822583X-RAY DIFFRACTION92
1.6471-1.69550.2741470.24122741X-RAY DIFFRACTION98
1.6955-1.75030.25011330.23242777X-RAY DIFFRACTION99
1.7503-1.81280.281470.23052761X-RAY DIFFRACTION98
1.8128-1.88540.25461580.20422765X-RAY DIFFRACTION99
1.8854-1.97120.23341250.19462822X-RAY DIFFRACTION100
1.9712-2.07520.22741410.19312817X-RAY DIFFRACTION99
2.0752-2.20520.25441350.18852772X-RAY DIFFRACTION98
2.2052-2.37540.23921530.18442797X-RAY DIFFRACTION99
2.3754-2.61440.22121480.19292836X-RAY DIFFRACTION99
2.6144-2.99270.19141510.19442799X-RAY DIFFRACTION99
2.9927-3.77020.18391490.18082848X-RAY DIFFRACTION99
3.7702-44.11020.17611410.18082934X-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)
13.3775-0.5168-0.90621.47890.00362.83730.16310.26770.1458-0.1052-0.0737-0.21470.00850.4583-0.06750.140.0309-0.00010.1935-0.00050.1742-15.0114.2091-1.5639
22.25820.36791.00672.44490.80226.51990.1163-0.48790.07620.4441-0.06530.1622-0.1866-0.2479-0.02320.3466-0.03210.03240.2613-0.02480.196-21.9-2.929631.6983
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