[English] 日本語
Yorodumi
- PDB-4al6: Crystal structure of the S148ACsy4-crRNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4al6
TitleCrystal structure of the S148ACsy4-crRNA complex
Components
  • CRRNA, 5'-R(CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP* CP*AP*GP*C)-3'
  • CSY4 ENDORIBONUCLEASE
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / CRISPR
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
CRISPR-associated endoribonuclease Cas6/Csy4 / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR-associated endonuclease Cas6/Csy4
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsHaurwitz, R.E. / Sternberg, S.H. / Doudna, J.A.
CitationJournal: Embo J. / Year: 2012
Title: Csy4 Relies on an Unusual Catalytic Dyad to Position and Cleave Crispr RNA.
Authors: Haurwitz, R.E. / Sternberg, S.H. / Doudna, J.A.
History
DepositionMar 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CSY4 ENDORIBONUCLEASE
B: CRRNA, 5'-R(CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP* CP*AP*GP*C)-3'


Theoretical massNumber of molelcules
Total (without water)26,9172
Polymers26,9172
Non-polymers00
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-9.1 kcal/mol
Surface area10260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.390, 46.880, 87.390
Angle α, β, γ (deg.)90.00, 107.24, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

-
Components

#1: Protein CSY4 ENDORIBONUCLEASE


Mass: 21803.910 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: UCBPP-PA14 / Plasmid: PHMGWA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q02MM2
#2: RNA chain CRRNA, 5'-R(CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP* CP*AP*GP*C)-3'


Mass: 5113.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE UNIPROT DATABASE SEQUENCE IS BASED ON AN INCORRECT START CODON. THE DATABASE SEQUENCE IS 20 ...THE UNIPROT DATABASE SEQUENCE IS BASED ON AN INCORRECT START CODON. THE DATABASE SEQUENCE IS 20 AMINO ACIDS SHORTER THAN THE ACTUAL POLYPEPTIDE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 45.78 % / Description: NONE
Crystal growpH: 5
Details: 20% PEG 4000, 150 MM NA CITRATE PH 5.0, 100 MM MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.63→41.73 Å / Num. obs: 8517 / % possible obs: 99.7 % / Observed criterion σ(I): 2.01 / Redundancy: 5.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.44
Reflection shellResolution: 2.63→2.7 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.54 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AL5

4al5


Resolution: 2.63→41.733 Å / SU ML: 0.34 / σ(F): 2.01 / Phase error: 24.61 / Stereochemistry target values: ML
Details: RESIDUES -4 TO -3 AND 106 TO 137 IN CHAIN A ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2521 368 5.1 %
Rwork0.2004 --
obs0.2031 7275 99.33 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.218 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--20.1319 Å20 Å28.8633 Å2
2---11.5082 Å20 Å2
3----17.0997 Å2
Refinement stepCycle: LAST / Resolution: 2.63→41.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 314 0 30 1516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161557
X-RAY DIFFRACTIONf_angle_d1.4772192
X-RAY DIFFRACTIONf_dihedral_angle_d16.498595
X-RAY DIFFRACTIONf_chiral_restr0.079254
X-RAY DIFFRACTIONf_plane_restr0.008232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6301-3.01060.28831240.23582291X-RAY DIFFRACTION100
3.0106-3.79260.28281210.19432283X-RAY DIFFRACTION99
3.7926-41.73780.22261230.19162333X-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)
10.23730.0052-0.04240.2109-0.07720.1551-0.19020.32450.14050.00740.1766-0.0197-0.00890.0063-0.00230.2212-0.0294-0.03760.2271-0.00610.288512.60182.013429.3095
20.0041-0.00450.00160.1063-0.07290.16190.04640.1017-0.0491-0.24490.0316-0.0029-0.0188-0.20210.08581.365-0.00820.48052.0076-0.03520.631618.8766-4.66016.2813
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID -1:104) OR (RESID 138:187)
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