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- PDB-3ufc: Characterization of a Cas6-related gene from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 3ufc
TitleCharacterization of a Cas6-related gene from Pyrococcus furiosus
ComponentsPutative uncharacterized protein
KeywordsHYDROLASE / Cas6 / Ferredoxin-like domain / RNA binding
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / defense response to virus / RNA binding
Similarity search - Function
: / CRISPR associated protein Cas6, C-terminal / CRISPR-associated protein Cas6, N-terminal / Alpha-Beta Plaits - #1890 / CRISPR-associated protein Cas6, N-terminal domain superfamily / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Putative CRISPR-associated endoribonuclease-like protein Cas6
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsPark, H.M. / Kim, J.S.
CitationJournal: Proteins / Year: 2012
Title: Crystal structure of a Cas6 paralogous protein from Pyrococcus furiosus
Authors: Park, H.M. / Shin, M. / Sun, J. / Kim, G.S. / Lee, Y.C. / Park, J.H. / Kim, B.Y. / Kim, J.S.
History
DepositionNov 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)28,2031
Polymers28,2031
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.805, 79.805, 117.362
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative uncharacterized protein / Cas6


Mass: 28203.010 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8U3R3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.83 Å3/Da / Density % sol: 67.85 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (w/v) polyethylene glycol 400, 0.1M HEPES-Na, 0.1M Magnesium chloride hexahydrate , pH 7.5, 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: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 31, 2011
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. all: 28593 / Num. obs: 26932 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.6 %
Reflection shellResolution: 2.09→2.18 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2275 2166 7.6 %RANDOM
Rwork0.203 ---
all0.2275 28593 --
obs0.203 26932 94.2 %-
Solvent computationksol: 102.934 e/Å3
Displacement parametersBiso max: 92.66 Å2 / Biso mean: 37.7029 Å2 / Biso min: 16.09 Å2
Baniso -1Baniso -2Baniso -3
1-4.409 Å20 Å20 Å2
2--4.409 Å20 Å2
3----8.819 Å2
Refinement stepCycle: LAST / Resolution: 2.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 0 179 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.257
X-RAY DIFFRACTIONc_mcbond_it1.6231.5
X-RAY DIFFRACTIONc_scbond_it2.3482
X-RAY DIFFRACTIONc_mcangle_it2.6292
X-RAY DIFFRACTIONc_scangle_it3.7242.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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