[English] 日本語
Yorodumi
- PDB-5vvk: Cas1-Cas2 bound to full-site mimic -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5vvk
TitleCas1-Cas2 bound to full-site mimic
DescriptorCRISPR-associated endonuclease Cas1
CRISPR-associated endoribonuclease Cas2/DNA Complex
KeywordsHYDROLASE/DNA / Complex / DNA / HYDROLASE-DNA complex
Specimen sourceEscherichia coli (strain k12) / bacteria /
Synthetic construct
MethodX-ray diffraction (2.9 Å resolution / Molecular replacement)
AuthorsWright, A.V. / Knott, G.J. / Doxzen, K.D. / Doudna, J.A.
CitationScience, 2017

Science, 2017 StrPapers
Structures of the CRISPR genome integration complex.
Wright, A.V. / Liu, J.J. / Knott, G.J. / Doxzen, K.W. / Nogales, E. / Doudna, J.A.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 19, 2017 / Release: Aug 2, 2017

-
Structure visualization

3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1
B: CRISPR-associated endonuclease Cas1
C: CRISPR-associated endonuclease Cas1
D: CRISPR-associated endonuclease Cas1
E: CRISPR-associated endoribonuclease Cas2
F: CRISPR-associated endoribonuclease Cas2
G: DNA (5'-D(*GP*CP*CP*CP*CP*AP*GP*TP*AP*GP*C)-3')
H: DNA (5'-D(*GP*AP*CP*CP*AP*CP*CP*AP*GP*TP*G)-3')
J: DNA (58-MER)
K: DNA (58-MER)


Theoretical massNumber of molelcules
Total (without water)197,87510
Polyers197,87510
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)28890
ΔGint (kcal/M)-181
Surface area (Å2)64240
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)74.900, 197.612, 95.344
Angle α, β, γ (deg.)90.000, 112.700, 90.000
Int Tables number4
Space group name H-MP 1 21 1

-
Components

-
CRISPR-associated ... , 2 types, 6 molecules ABCDEF

#1: Polypeptide(L)
CRISPR-associated endonuclease Cas1


Mass: 33570.770 Da / Num. of mol.: 4 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: Q46896, EC: 3.1.-.-
#2: Polypeptide(L)CRISPR-associated endoribonuclease Cas2


Mass: 10527.212 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P45956, EC: 3.1.-.-

-
DNA chain , 4 types, 4 molecules GHJK

#3: DNA chainDNA (5'-D(*GP*CP*CP*CP*CP*AP*GP*TP*AP*GP*C)-3')


Mass: 3319.175 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#4: DNA chainDNA (5'-D(*GP*AP*CP*CP*AP*CP*CP*AP*GP*TP*G)-3')


Mass: 3343.200 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#5: DNA chainDNA (58-MER)


Mass: 17907.432 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#6: DNA chainDNA (58-MER)


Mass: 17967.461 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 / Density percent sol: 62.61 / Description: Rectangular plates
Crystal growTemp: 291 K / Method: VAPOR DIFFUSION, SITTING DROP / pH: 6.4 / Details: 100 mM MES pH, 20% (w/v) PEG MME 2000, 0.2 M NaCl

-
Data collection

DiffractionMean temperature: 80 kelvins
SourceSource: SYNCHROTRON / Type: ALS BEAMLINE 8.3.1 / Synchrotron site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Collection date: Apr 14, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 76.73 Å2 / D resolution high: 2.76 Å / D resolution low: 197.61 Å / Number obs: 64543 / CC half: 0.998 / Rmerge I obs: 0.146 / Rpim I all: 0.059 / Rrim I all: 0.158 / NetI over sigmaI: 10.4 / Redundancy: 7.2 / Percent possible obs: 98.1
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionCC halfRpim I allRrim I allRedundancyPercent possible all
3.6892.7602.8300.2481.6374.0555.30074.600
0.02712.640197.6100.9990.0110.0296.90099.500

-
Phasing

PhasingMethod: MR

-
Processing

Software
NameVersionClassification
Aimless0.5.31data scaling
PHENIX1.11.1refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DS5
Overall SU ML: 0.49 / Cross valid method: FREE R-VALUE / Sigma F: 1.34 / Overall phase error: 31.8
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 285.18 Å2 / B iso mean: 101.7096 Å2 / B iso min: 31 Å2
Least-squares processR factor R free: 0.2536 / R factor R work: 0.2166 / R factor obs: 0.2185 / Highest resolution: 2.9 Å / Lowest resolution: 98.806 Å / Number reflection R free: 2914 / Number reflection obs: 56364 / Percent reflection R free: 5.17 / Percent reflection obs: 99.77
Refine hist #finalHighest resolution: 2.9 Å / Lowest resolution: 98.806 Å / Number residues total: 1364
Number of atoms included #finalProtein: 9688 / Nucleic acid: 2208 / Ligand: 0 / Solvent: 0 / Total: 11896
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312347
X-RAY DIFFRACTIONf_angle_d0.53317199
X-RAY DIFFRACTIONf_chiral_restr0.0381970
X-RAY DIFFRACTIONf_plane_restr0.0041829
X-RAY DIFFRACTIONf_dihedral_angle_d17.2767014
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 21

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
2.90000.49420.46492.94761102509261999.0000
2.94760.44010.42172.998412225972719100.0000
2.99840.42280.36323.052915924892648100.0000
3.05290.39390.34683.111613225822714100.0000
3.11160.33420.30673.175212825352663100.0000
3.17520.30380.27803.244215825132671100.0000
3.24420.30670.26893.319714025252665100.0000
3.31970.30310.26023.402713725782715100.0000
3.40270.29080.24523.494716624602626100.0000
3.49470.30540.23663.597515325392692100.0000
3.59750.27690.23403.71371442520266499.0000
3.71370.26460.22023.846411025832693100.0000
3.84640.26040.20484.000415525532708100.0000
4.00040.22600.19084.182513925322671100.0000
4.18250.22310.17624.403013725492686100.0000
4.40300.22740.16794.678815125492700100.0000
4.67880.18920.17615.040113825492687100.0000
5.04010.25880.18735.547312425562680100.0000
5.54730.22390.21006.349815825542712100.0000
6.34980.20690.20407.999614025652705100.0000
7.99960.20350.179498.86331132613272699.0000

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more