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- PDB-4gkf: Crystal structure and characterization of Cmr5 protein from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 4gkf
TitleCrystal structure and characterization of Cmr5 protein from Pyrococcus furiosus
ComponentsCRISPR system Cmr subunit Cmr5
KeywordsUNKNOWN FUNCTION / Crispr
Function / homology
Function and homology information


defense response to virus / cytoplasm
Similarity search - Function
AF1862-like domain / CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, Cmr5 / AF1862-like domain superfamily / Peroxidase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CRISPR system Cmr subunit Cmr5
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPark, J. / Sun, J. / Park, S. / Hwang, H. / Park, M. / Shin, M.S.
CitationJournal: Febs Lett. / Year: 2013
Title: Crystal structure of Cmr5 from Pyrococcus furiosus and its functional implications
Authors: Park, J.H. / Sun, J. / Park, S.Y. / Hwang, H.J. / Park, M.Y. / Shin, M. / Kim, J.S.
History
DepositionAug 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR system Cmr subunit Cmr5
B: CRISPR system Cmr subunit Cmr5


Theoretical massNumber of molelcules
Total (without water)39,4342
Polymers39,4342
Non-polymers00
Water3,315184
1
A: CRISPR system Cmr subunit Cmr5


Theoretical massNumber of molelcules
Total (without water)19,7171
Polymers19,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CRISPR system Cmr subunit Cmr5


Theoretical massNumber of molelcules
Total (without water)19,7171
Polymers19,7171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.944, 53.944, 235.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CRISPR system Cmr subunit Cmr5 / CRISPR type III-B/RAMP module-associated protein Cmr5


Mass: 19716.793 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cmr5, PF1125 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1T0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.18 Å3/Da / Density % sol: 43.49 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 %(w/v) Polyethylene Glycol 3350, 0.1M Bis-Tris HCl, 0.2M Magnesium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2011
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 23080 / % possible obs: 93.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2.1→2.15 Å / % possible all: 91

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2oeb

2oeb


Resolution: 2.1→49.06 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2758 1294 RANDOM
Rwork0.2173 --
obs0.2173 17956 -
all-19250 -
Refinement stepCycle: LAST / Resolution: 2.1→49.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2421 0 0 184 2605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.07383
X-RAY DIFFRACTIONc_bond_d0.005794

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