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- PDB-4n06: Crystal structure of Cas1 from Archaeoglobus fulgidus and its nuc... -

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Basic information

Entry
Database: PDB / ID: 4n06
TitleCrystal structure of Cas1 from Archaeoglobus fulgidus and its nucleolytic activity
ComponentsCRISPR-associated endonuclease Cas1 1
KeywordsHYDROLASE
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding
Similarity search - Function
CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle ...CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR-associated endonuclease Cas1, N-terminal domain / CRISPR-associated protein Cas1 / CRISPR-associated endonuclease Cas1, C-terminal domain / CRISPR associated protein Cas1 / Ribosomal Protein L15; Chain: K; domain 2 / Ribosomal Protein L15; Chain: K; domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endonuclease Cas1 1
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKim, T.Y. / Shin, M. / Yen, L.H.T. / Kim, J.S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystal structure of Cas1 from Archaeoglobus fulgidus and characterization of its nucleolytic activity
Authors: Kim, T.Y. / Shin, M. / Yen, L.H.T. / Kim, J.S.
History
DepositionOct 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated endonuclease Cas1 1
B: CRISPR-associated endonuclease Cas1 1


Theoretical massNumber of molelcules
Total (without water)79,1022
Polymers79,1022
Non-polymers00
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-18 kcal/mol
Surface area30290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.886, 41.929, 125.293
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR-associated endonuclease Cas1 1


Mass: 39550.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
References: UniProt: O28401, Hydrolases; Acting on ester bonds
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30%(w/v) Polyethyleneglycol Monomethylether 550, 0.1M Bicine, 0.1M Sodium Chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9897 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9897 Å / Relative weight: 1
ReflectionResolution: 2.4→65.116 Å / Num. all: 80121 / Num. obs: 28962 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.4→2.47 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→65.116 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 23.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2413 1738 6 %
Rwork0.1985 --
obs0.2011 28947 99.36 %
all-29132 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→65.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5491 0 0 355 5846
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035565
X-RAY DIFFRACTIONf_angle_d0.7547465
X-RAY DIFFRACTIONf_dihedral_angle_d13.6622161
X-RAY DIFFRACTIONf_chiral_restr0.055841
X-RAY DIFFRACTIONf_plane_restr0.004957
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.47070.30431440.25062251X-RAY DIFFRACTION100
2.4707-2.55040.31781420.25112236X-RAY DIFFRACTION100
2.5504-2.64160.32611450.23612272X-RAY DIFFRACTION100
2.6416-2.74740.25621440.2272253X-RAY DIFFRACTION100
2.7474-2.87240.28351420.22352225X-RAY DIFFRACTION99
2.8724-3.02380.30921430.21892247X-RAY DIFFRACTION99
3.0238-3.21330.25051480.20842298X-RAY DIFFRACTION100
3.2133-3.46140.25021430.19222246X-RAY DIFFRACTION100
3.4614-3.80970.21041450.17792266X-RAY DIFFRACTION99
3.8097-4.36080.20091440.16012264X-RAY DIFFRACTION99
4.3608-5.49380.18711470.1672296X-RAY DIFFRACTION99
5.4938-65.13980.21731510.20342355X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 9.8602 Å / Origin y: 1.8998 Å / Origin z: 33.2222 Å
111213212223313233
T0.0942 Å20.0012 Å2-0.0032 Å2-0.0389 Å2-0.0169 Å2--0.0582 Å2
L0.0989 °2-0.0384 °20.0116 °2--0.1326 °2-0.1459 °2--0.5266 °2
S0.028 Å °0.0135 Å °0.0269 Å °-0.1599 Å °-0.0595 Å °-0.0233 Å °0.1069 Å °0.1371 Å °-0.0243 Å °
Refinement TLS groupSelection details: all

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