[English] 日本語
Yorodumi
- PDB-4r5q: Crystal structure and nuclease activity of the CRISPR-associated ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4r5q
TitleCrystal structure and nuclease activity of the CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis containing a [2Fe-2S] cluster
ComponentsCRISPR-associated exonuclease, Cas4 family
KeywordsHYDROLASE / MCSG / STRUCTURAL GENOMICS / PSI-BIOLOGY / EXONUCLEASE / Midwest Center for Structural Genomics
Function / homology
Function and homology information


5' to 3' exodeoxyribonuclease (nucleoside 3'-phosphate-forming) / single-stranded DNA 5'-3' DNA exonuclease activity / single-stranded DNA endodeoxyribonuclease activity / DNA duplex unwinding / 2 iron, 2 sulfur cluster binding / defense response to virus / metal ion binding
Similarity search - Function
CRISPR-associated protein Cas4 / Lambda Exonuclease; Chain A - #10 / Dna2/Cas4, domain of unknown function DUF83 / Domain of unknown function DUF83 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FE2/S2 (INORGANIC) CLUSTER / CRISPR-associated exonuclease Cas4
Similarity search - Component
Biological speciesPyrobaculum calidifontis JCM 11548 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsNocek, B. / Skarina, T. / Lemak, S. / Brown, G. / Savchenko, A. / Joachimiak, A. / Yakunin, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure and nuclease activity of the CRISPR-associated Cas4 protein Pcal_0546 from Pyrobaculum calidifontis containing a [2Fe-2S] cluster
Authors: Nocek, B. / Skarina, T. / Lemak, S. / Brown, G. / Savchenko, A. / Joachimiak, A. / Yakunin, A.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionSep 17, 2014ID: 4ONB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated exonuclease, Cas4 family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2313
Polymers25,0311
Non-polymers2002
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.836, 117.836, 89.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

DetailsSolution and crystallographic studies indicate monomer as most likely oligomeric state. SEC experiment shows that this protein is a monomer in the solution.

-
Components

#1: Protein CRISPR-associated exonuclease, Cas4 family


Mass: 25031.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum calidifontis JCM 11548 (archaea)
Strain: JCM 11548 / VA1 / Gene: Pcal_0546 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: A3MTK6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER / Iron–sulfur cluster


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 3.1 Å3/Da / Density % sol: 60.32 %
Crystal growTemperature: 293 K / pH: 7
Details: 3.5M Sodium FORMATE, 0.1M BIS-TRIS PROPANE, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2012 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.65→37.26 Å / Num. obs: 9378 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 41

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
DMmodel building
SHELXmodel building
Cootmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.65→37.26 Å / SU ML: 0.34 / σ(F): 3 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.253 651 4.76 %
Rwork0.228 --
obs0.229 9155 99.1 %
all-9378 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→37.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1711 0 5 21 1737
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011759
X-RAY DIFFRACTIONf_angle_d0.6322368
X-RAY DIFFRACTIONf_dihedral_angle_d14.45659
X-RAY DIFFRACTIONf_chiral_restr0.028269
X-RAY DIFFRACTIONf_plane_restr0.003303
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.85570.3864830.36741576X-RAY DIFFRACTION47
2.8557-3.14290.35681200.30822012X-RAY DIFFRACTION61
3.1429-3.59740.29921380.24422893X-RAY DIFFRACTION88
3.5974-4.53110.20781560.19883298X-RAY DIFFRACTION99
4.5311-37.26670.20771540.19943237X-RAY DIFFRACTION97
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)
14.4564-0.95330.08632.47750.29372.23080.0784-0.13830.34260.21270.0803-0.0503-0.5243-0.2667-0.11360.64770.2040.27590.4840.04240.4974-1.7209-20.7067-4.6934
25.3842-2.8275-1.21445.22773.56677.10950.3248-0.21980.3871-0.0125-0.1496-0.4311-0.38520.6662-0.09990.3107-0.08840.15690.4561-0.15330.460420.9589-28.4109-10.0368
31.1931-0.0894-0.66240.3086-0.09671.02580.16690.21960.1237-0.0828-0.05930.0032-0.2771-0.37270.05880.28150.02470.27380.341-0.13410.360113.7338-29.8806-25.1499
44.1744-0.5866-1.70740.54930.70391.89010.0766-0.07030.07130.01390.033-0.0304-0.11680.0334-0.03070.29810.10740.17520.3314-0.02430.25774.6646-25.8007-8.5641
53.90190.3184-1.2231.7067-1.18724.00910.11260.6028-0.3327-0.2795-0.01820.00260.0264-0.73470.18390.31890.25380.09390.7734-0.03830.342-5.7286-30.2308-19.0081
63.9245-1.0238-2.02590.71680.76891.17650.29321.25490.0088-0.678-0.2121-0.0713-0.6563-0.8076-0.06620.58570.19120.17660.73720.01120.47764.8215-25.3087-28.7588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 42 )
3X-RAY DIFFRACTION3chain 'A' and (resid 43 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 101 )
5X-RAY DIFFRACTION5chain 'A' and (resid 102 through 157 )
6X-RAY DIFFRACTION6chain 'A' and (resid 158 through 212 )

+
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