[English] 日本語
Yorodumi
- PDB-6h9h: Csf5, CRISPR-Cas type IV Cas6 crRNA endonuclease -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6h9h
TitleCsf5, CRISPR-Cas type IV Cas6 crRNA endonuclease
Components
  • Csf5Markerville/Safron Farms Aerodrome
  • crRNA
KeywordsRNA BINDING PROTEIN / type IV CRISPR-Cas / crRNA biogenesis / endonuclease
Function / homology: / L(+)-TARTARIC ACID / RNA / RNA (> 10) / DUF1460 domain-containing protein
Function and homology information
Biological speciesAromatoleum aromaticum (bacteria)
Aromatoleum aromaticum EbN1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsPausch, P. / Bange, G.
CitationJournal: Nat Microbiol / Year: 2019
Title: Type IV CRISPR RNA processing and effector complex formation in Aromatoleum aromaticum.
Authors: Ozcan, A. / Pausch, P. / Linden, A. / Wulf, A. / Schuhle, K. / Heider, J. / Urlaub, H. / Heimerl, T. / Bange, G. / Randau, L.
History
DepositionAug 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Csf5
A: Csf5
D: crRNA
E: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,89910
Polymers76,1524
Non-polymers7476
Water5,531307
1
B: Csf5
E: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,3735
Polymers38,0762
Non-polymers2973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-32 kcal/mol
Surface area14480 Å2
MethodPISA
2
A: Csf5
D: crRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5265
Polymers38,0762
Non-polymers4503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-32 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.563, 100.989, 101.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / RNA chain , 2 types, 4 molecules BADE

#1: Protein Csf5 / Markerville/Safron Farms Aerodrome


Mass: 29695.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aromatoleum aromaticum (strain EbN1) (bacteria)
Strain: EbN1 / Gene: p1B372 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5NWP0
#2: RNA chain crRNA


Mass: 8380.917 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aromatoleum aromaticum EbN1 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)

-
Non-polymers , 4 types, 313 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water / Water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.94 Å3/Da / Density % sol: 58.17 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.18 M di-ammonium tartrate, 18% w/v PEG3350, 3% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.75→45.25 Å / Num. obs: 89451 / % possible obs: 99.88 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.09 / Net I/σ(I): 20.32
Reflection shellResolution: 1.75→1.81 Å

-
Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.25 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.97
RfactorNum. reflection% reflection
Rfree0.2371 8528 4.96 %
Rwork0.2122 --
obs0.2135 89435 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3916 1001 47 307 5271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075241
X-RAY DIFFRACTIONf_angle_d1.1257342
X-RAY DIFFRACTIONf_dihedral_angle_d11.3393009
X-RAY DIFFRACTIONf_chiral_restr0.061863
X-RAY DIFFRACTIONf_plane_restr0.006773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.76990.38972840.34665414X-RAY DIFFRACTION100
1.7699-1.79070.36123020.32755440X-RAY DIFFRACTION100
1.7907-1.81260.34532750.32145472X-RAY DIFFRACTION100
1.8126-1.83550.32133050.30475402X-RAY DIFFRACTION100
1.8355-1.85970.32083580.29255425X-RAY DIFFRACTION100
1.8597-1.88510.3172990.29535358X-RAY DIFFRACTION100
1.8851-1.91210.32622840.29145470X-RAY DIFFRACTION100
1.9121-1.94060.31332950.28485423X-RAY DIFFRACTION100
1.9406-1.97090.33843110.27595414X-RAY DIFFRACTION100
1.9709-2.00320.27872360.26395455X-RAY DIFFRACTION100
2.0032-2.03780.30082800.26115489X-RAY DIFFRACTION100
2.0378-2.07480.29132710.25685433X-RAY DIFFRACTION100
2.0748-2.11470.29522920.25295482X-RAY DIFFRACTION100
2.1147-2.15790.27423080.24985380X-RAY DIFFRACTION100
2.1579-2.20480.2692890.24655470X-RAY DIFFRACTION100
2.2048-2.25610.28522670.23275465X-RAY DIFFRACTION100
2.2561-2.31250.25842840.23375432X-RAY DIFFRACTION100
2.3125-2.37510.3022750.2465449X-RAY DIFFRACTION100
2.3751-2.44490.28782590.24415457X-RAY DIFFRACTION100
2.4449-2.52390.3162170.24885523X-RAY DIFFRACTION100
2.5239-2.61410.26122540.23575476X-RAY DIFFRACTION100
2.6141-2.71870.24322870.2315408X-RAY DIFFRACTION100
2.7187-2.84240.24142800.22555452X-RAY DIFFRACTION100
2.8424-2.99230.24053020.21365459X-RAY DIFFRACTION100
2.9923-3.17970.24642890.21085438X-RAY DIFFRACTION100
3.1797-3.42510.22642800.21035446X-RAY DIFFRACTION100
3.4251-3.76960.21622410.19555497X-RAY DIFFRACTION100
3.7696-4.31480.19332870.1755446X-RAY DIFFRACTION100
4.3148-5.43470.19013020.16295392X-RAY DIFFRACTION100
5.4347-45.51580.19313150.17765412X-RAY DIFFRACTION100

+
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