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- PDB-5vvl: Cas1-Cas2 bound to full-site mimic with Ni -

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Basic information

Entry
Database: PDB / ID: 5vvl
TitleCas1-Cas2 bound to full-site mimic with Ni
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 (3.31 Å resolution / Molecular replacement)
AuthorsWright, A.V. / Knott, G.J. / Doxzen, K.D. / Doudna, J.A.
CitationScience, 2017, 357, 1113-1118

Science, 2017, 357, 1113-1118 Yorodumi Papers
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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 2, 2017Structure modelrepositoryInitial release
1.1Sep 27, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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 (11-MER)
H: DNA (11-MER)
J: DNA (58-MER)
K: DNA (58-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,21832
Polyers199,92710
Non-polymers1,29122
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)31540
ΔGint (kcal/M)-368
Surface area (Å2)62550
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)74.642, 197.728, 88.792
Angle α, β, γ (deg.)90.000, 111.350, 90.000
Int Tables number4
Space group name H-MP 1 21 1

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Components

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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.-.-

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)CRISPR-associated endoribonuclease Cas2


Mass: 11553.270 Da / Num. of mol.: 2 / Source: (gene. exp.) Escherichia coli (strain K12) / References: UniProt: P45956, EC: 3.1.-.-

Molecular function

Biological process

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DNA chain , 4 types, 4 molecules GHJK

#3: DNA chainDNA (11-MER)


Mass: 3319.175 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct
#4: DNA chainDNA (11-MER)


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

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Non-polymers , 1 types, 22 molecules

#7: Chemical...
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 22 / Formula: Ni

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.33 / Density percent sol: 63.08
Crystal growTemp: 281 K / Method: VAPOR DIFFUSION, HANGING DROP / pH: 6.4
Details: 100 mM MES pH 6.4, 20% (w/v) PEG MME 2000, 0.2 M NaCl, 3 mM NiCl2

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Data collection

DiffractionMean temperature: 80 kelvins
SourceSource: SYNCHROTRON / Type: SSRL BEAMLINE BL9-2 / Synchrotron site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Collection date: Mar 4, 2017
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 92.52 Å2 / D resolution high: 2.96 Å / D resolution low: 39.55 Å / Number obs: 47810 / CC half: 0.996 / Rmerge I obs: 0.203 / Rpim I all: 0.083 / Rrim I all: 0.22 / NetI over sigmaI: 7.9 / Number measured all: 329343 / Redundancy: 6.9 / Scaling rejects: 0 / Percent possible obs: 96.3
Reflection shell

Diffraction ID: 1

Rmerge I obsHighest resolutionLowest resolutionCC halfRpim I allRrim I allRedundancyPercent possible all
4.4102.9603.0700.2151.8424.7926.30071.800
0.03711.48039.5500.9990.0160.0406.50095.700

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Phasing

PhasingMethod: MR

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Aimless0.5.31data scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DS5
Overall SU ML: 0.47 / Cross valid method: FREE R-VALUE / Sigma F: 1.33 / Overall phase error: 28.46
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å
Displacement parametersB iso max: 328.62 Å2 / B iso mean: 106.5272 Å2 / B iso min: 46.84 Å2
Least-squares processR factor R free: 0.2629 / R factor R work: 0.2243 / R factor obs: 0.2262 / Highest resolution: 3.31 Å / Lowest resolution: 39.504 Å / Number reflection R free: 1833 / Number reflection obs: 35241 / Percent reflection R free: 5.2 / Percent reflection obs: 98.83
Refine hist #finalHighest resolution: 3.31 Å / Lowest resolution: 39.504 Å / B iso mean ligand: 131.45 / Number residues total: 1361
Number of atoms included #finalProtein: 9757 / Nucleic acid: 1983 / Ligand: 22 / Solvent: 0 / Total: 11762
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312166
X-RAY DIFFRACTIONf_angle_d0.49316903
X-RAY DIFFRACTIONf_chiral_restr0.0371932
X-RAY DIFFRACTIONf_plane_restr0.0031832
X-RAY DIFFRACTIONf_dihedral_angle_d16.6966941
Refine LS shell

Refine ID: X-RAY DIFFRACTION / R factor R free error: 0 / Total number of bins used: 13

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workNumber reflection allPercent reflection obs
3.31000.37020.35333.39951602543270399.0000
3.39950.36830.32613.49941622509267199.0000
3.49940.32200.30473.61231372557269499.0000
3.61230.33860.30023.74131342610274499.0000
3.74130.32920.26393.89101352559269499.0000
3.89100.27360.24294.06791452549269499.0000
4.06790.28240.21764.28211292561269099.0000
4.28210.21670.19444.550114725692716100.0000
4.55010.19420.17884.90081402606274699.0000
4.90080.25540.20585.39291362559269599.0000
5.39290.30910.22546.17071482590273899.0000
6.17070.25760.20817.76471452578272399.0000
7.76470.19000.188439.50641152618273398.0000

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