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- PDB-4w8v: Crystal structure of Cmr6 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 4w8v
TitleCrystal structure of Cmr6 from Pyrococcus furiosus
ComponentsCRISPR system Cmr subunit Cmr6
KeywordsRNA BINDING PROTEIN / CMR complex
Function / homologyCRISPR-associated protein, TM1791 / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA binding / cytoplasm / CRISPR system Cmr subunit Cmr6
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsBenda, C. / Ebert, J. / Baumgaertner, M. / Conti, E.
CitationJournal: Mol.Cell / Year: 2014
Title: Structural Model of a CRISPR RNA-Silencing Complex Reveals the RNA-Target Cleavage Activity in Cmr4.
Authors: Benda, C. / Ebert, J. / Scheltema, R.A. / Schiller, H.B. / Baumgartner, M. / Bonneau, F. / Mann, M. / Conti, E.
History
DepositionAug 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR system Cmr subunit Cmr6
B: CRISPR system Cmr subunit Cmr6


Theoretical massNumber of molelcules
Total (without water)55,8302
Polymers55,8302
Non-polymers00
Water3,495194
1
A: CRISPR system Cmr subunit Cmr6


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CRISPR system Cmr subunit Cmr6


Theoretical massNumber of molelcules
Total (without water)27,9151
Polymers27,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.396, 127.731, 133.303
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-445-

HOH

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Components

#1: Protein CRISPR system Cmr subunit Cmr6 / CRISPR type III-B/RAMP module RAMP protein Cmr6


Mass: 27915.160 Da / Num. of mol.: 2 / Fragment: UNP residues 101-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cmr6, PF1124
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8U1T1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 2.4 M sodium malonate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99994 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 2.15→66.65 Å / Num. obs: 64400 / % possible obs: 99.51 % / Redundancy: 13.2 % / Net I/σ(I): 26.47
Reflection shellResolution: 2.15→2.227 Å / Redundancy: 12 % / Mean I/σ(I) obs: 1.01 / % possible all: 95.13

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1678)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.15→66.651 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 3239 5.03 %random selection
Rwork0.1756 ---
obs0.1784 64400 99.15 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→66.651 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3693 0 0 194 3887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083795
X-RAY DIFFRACTIONf_angle_d1.0455136
X-RAY DIFFRACTIONf_dihedral_angle_d13.9291422
X-RAY DIFFRACTIONf_chiral_restr0.041570
X-RAY DIFFRACTIONf_plane_restr0.005657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1504-2.18250.42421150.39442254X-RAY DIFFRACTION85
2.1825-2.21660.41681410.3642674X-RAY DIFFRACTION99
2.2166-2.2530.38851470.362713X-RAY DIFFRACTION99
2.253-2.29180.37881410.33772648X-RAY DIFFRACTION100
2.2918-2.33350.33051410.3222655X-RAY DIFFRACTION99
2.3335-2.37840.36661400.30482640X-RAY DIFFRACTION99
2.3784-2.42690.33771450.29742695X-RAY DIFFRACTION100
2.4269-2.47970.31571450.29462700X-RAY DIFFRACTION100
2.4797-2.53740.30031390.26852669X-RAY DIFFRACTION100
2.5374-2.60080.26111430.24462680X-RAY DIFFRACTION100
2.6008-2.67110.30441400.24562666X-RAY DIFFRACTION100
2.6711-2.74980.32511420.25472684X-RAY DIFFRACTION100
2.7498-2.83850.29851430.23772668X-RAY DIFFRACTION100
2.8385-2.940.36681380.21062677X-RAY DIFFRACTION100
2.94-3.05770.23531380.20642646X-RAY DIFFRACTION100
3.0577-3.19680.27071430.18752735X-RAY DIFFRACTION100
3.1968-3.36540.25461380.18722653X-RAY DIFFRACTION100
3.3654-3.57620.25921460.17132700X-RAY DIFFRACTION100
3.5762-3.85230.21921390.14922668X-RAY DIFFRACTION100
3.8523-4.23990.19251460.12942676X-RAY DIFFRACTION100
4.2399-4.85330.1581390.11822689X-RAY DIFFRACTION100
4.8533-6.1140.19241420.14822683X-RAY DIFFRACTION100
6.114-66.68350.18981480.15232688X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.9593 Å / Origin y: 10.7156 Å / Origin z: -20.5601 Å
111213212223313233
T0.4678 Å2-0.0139 Å20.0322 Å2-0.4477 Å2-0.0215 Å2--0.4554 Å2
L0.9694 °2-0.2471 °20.4277 °2-0.7768 °2-0.0886 °2--0.8871 °2
S0.0985 Å °-0.0852 Å °0.0615 Å °-0.0646 Å °-0.0576 Å °0.1296 Å °0.0467 Å °0.0759 Å °0 Å °
Refinement TLS groupSelection details: all

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