[English] 日本語
Yorodumi
- PDB-6o6y: Crystal structure of Csm6 in complex with cyclic-tetraadenylates ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o6y
TitleCrystal structure of Csm6 in complex with cyclic-tetraadenylates (cA4) by cocrystallization of Csm6 and cA4
ComponentsCsm6
KeywordsIMMUNE SYSTEM / Type III-A CRISPR-Cas system / Csm6 in complex with cA4 by cocrystallization of Csm6 and cA4
Function / homologyCRISPR system endoribonuclease Csx1, HEPN domain / CRISPR system endoribonuclease Csx1 / CRISPR-associated protein DxTHG, conserved site / : / CRISPR system endoribonuclease Csx1, CARF domain / : / 2',3'- cyclic AMP / Chem-LQJ / CRISPR system endoribonuclease Csx1 CARF domain-containing protein
Function and homology information
Biological speciesThermococcus onnurineus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsJia, N. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2019
Title: CRISPR-Cas III-A Csm6 CARF Domain Is a Ring Nuclease Triggering Stepwise cA4Cleavage with ApA>p Formation Terminating RNase Activity.
Authors: Jia, N. / Jones, R. / Yang, G. / Ouerfelli, O. / Patel, D.J.
History
DepositionMar 7, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 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
A: Csm6
B: Csm6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5656
Polymers99,5902
Non-polymers1,9754
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-25 kcal/mol
Surface area34750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.451, 163.963, 111.105
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Csm6


Mass: 49795.113 Da / Num. of mol.: 2 / Mutation: H132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus onnurineus (archaea) / Strain: NA1 / Gene: TON_0898 / Production host: Escherichia coli (E. coli) / References: UniProt: B6YWC3
#2: Chemical ChemComp-ACK / 2',3'- cyclic AMP


Mass: 329.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N5O6P
#3: Chemical ChemComp-LQJ / 3'-O-[(R)-{[(2S,3aS,4S,6S,6aS)-6-(6-amino-9H-purin-9-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methoxy}(hydroxy)phosphoryl]adenosine


Mass: 658.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsLQJ is a result of cA4 cleavage occurred during crystallization

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 10% PEG 8K, 0.2 M NaCl, 0.1 M Na/K phosphate pH 6.2

-
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 PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 67441 / % possible obs: 99.5 % / Redundancy: 9.9 % / Rpim(I) all: 0.036 / Net I/σ(I): 17.2
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 6657

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→48.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.202 / SU ML: 0.164 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.177 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 6558 9.7 %RANDOM
Rwork0.20604 ---
obs0.21083 60862 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.683 Å2
Baniso -1Baniso -2Baniso -3
1-3.16 Å20 Å20 Å2
2---2.51 Å20 Å2
3----0.65 Å2
Refinement stepCycle: 1 / Resolution: 1.96→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 132 109 7131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0137191
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176848
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.6819763
X-RAY DIFFRACTIONr_angle_other_deg1.1471.59415836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.265863
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80520.981367
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69151253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3691558
X-RAY DIFFRACTIONr_chiral_restr0.0550.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021567
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5415.3133458
X-RAY DIFFRACTIONr_mcbond_other2.5415.3123457
X-RAY DIFFRACTIONr_mcangle_it3.8087.9634319
X-RAY DIFFRACTIONr_mcangle_other3.8087.9634320
X-RAY DIFFRACTIONr_scbond_it3.0795.9083732
X-RAY DIFFRACTIONr_scbond_other3.0795.9093733
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9848.6855445
X-RAY DIFFRACTIONr_long_range_B_refined7.12361.2777818
X-RAY DIFFRACTIONr_long_range_B_other7.12361.2697813
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.958→2.009 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 421 -
Rwork0.353 4150 -
obs--91.9 %

+
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