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- PDB-4ic1: Crystal structure of SSO0001 -

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Basic information

Entry
Database: PDB / ID: 4ic1
TitleCrystal structure of SSO0001
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Cas4 / CRISPR / MCSG / Exonuclease / PSI-Biology / 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 / DNA duplex unwinding / 4 iron, 4 sulfur cluster binding / manganese ion binding / defense response to virus / DNA binding
Similarity search - Function
CRISPR-associated protein Cas4 / Lambda Exonuclease; Chain A - #10 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain, AddAB-type / PD-(D/E)XK nuclease superfamily / PD-(D/E)XK endonuclease-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / IRON/SULFUR CLUSTER / CRISPR-associated exonuclease Cas4
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsNocek, B. / Skarina, T. / Lemak, S. / Beloglazova, N. / Flick, R. / Brown, G. / Savchenko, A. / Joachimiak, A. / Yakunin, A.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Toroidal structure and DNA cleavage by the CRISPR-associated [4Fe-4S] cluster containing Cas4 nuclease SSO0001 from Sulfolobus solfataricus.
Authors: Lemak, S. / Beloglazova, N. / Nocek, B. / Skarina, T. / Flick, R. / Brown, G. / Popovic, A. / Joachimiak, A. / Savchenko, A. / Yakunin, A.F.
History
DepositionDec 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
F: Uncharacterized protein
G: Uncharacterized protein
H: Uncharacterized protein
I: Uncharacterized protein
J: Uncharacterized protein
K: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,13830
Polymers239,07210
Non-polymers4,06620
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area36630 Å2
ΔGint-543 kcal/mol
Surface area87500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.152, 197.761, 89.410
Angle α, β, γ (deg.)90.00, 100.88, 90.00
Int Tables number4
Space group name H-MP1211
Detailsconfirmed biologically

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Components

#1: Protein
Uncharacterized protein


Mass: 23907.211 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: SSO0001 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21DE3 / References: UniProt: Q97TX9
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Fe4S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 3350, 0.1M NaCitrate, 0.2M NaCl, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.9794
SYNCHROTRONAPS 19-BM21.738
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 315r1CCDOct 30, 2012mirrors
ADSC QUANTUM 2102CCDOct 30, 2012mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double CrystalSINGLE WAVELENGTHMx-ray1
2Double CrystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
21.7381
ReflectionResolution: 2.35→40 Å / Num. all: 121708 / Num. obs: 118972 / % possible obs: 97.3 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 25.6
Reflection shellResolution: 2.35→2.39 Å / % possible all: 94.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
Auto-Rickshawphasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.35→40 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.625 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 1.7 / σ(I): 2 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 5038 5 %RANDOM
Rwork0.20128 ---
all0.22 100633 --
obs0.20533 95585 82.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.708 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.37 Å2
2--0.3 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16077 0 90 292 16459
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.02216518
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211110
X-RAY DIFFRACTIONr_angle_refined_deg2.0921.98622470
X-RAY DIFFRACTIONr_angle_other_deg1.315327231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11252020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56324.026703
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.005152961
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.79115100
X-RAY DIFFRACTIONr_chiral_restr0.170.22649
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217872
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023208
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7181.510120
X-RAY DIFFRACTIONr_mcbond_other2.5861.54071
X-RAY DIFFRACTIONr_mcangle_it3.029216398
X-RAY DIFFRACTIONr_scbond_it3.95136398
X-RAY DIFFRACTIONr_scangle_it6.2854.55946
X-RAY DIFFRACTIONr_rigid_bond_restr2.276316389
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.347→2.408 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 82 -
Rwork0.21 1689 -
obs--19.72 %

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