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- PDB-4w8z: Crystal structure of Cmr1 from Pyrococcus furiosus (apo form) -

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Basic information

Entry
Database: PDB / ID: 4w8z
TitleCrystal structure of Cmr1 from Pyrococcus furiosus (apo form)
ComponentsCRISPR system Cmr subunit Cmr1-1
KeywordsRNA BINDING PROTEIN / Cmr1 / apo form / CMR complex / CRISPR
Function / homology: / Cmr1-like, C-terminal / CRISPR-associated protein TM1795 / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / RNA binding / cytoplasm / CRISPR system Cmr subunit Cmr1-1
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 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 1.1May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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 Cmr1-1


Theoretical massNumber of molelcules
Total (without water)39,7831
Polymers39,7831
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.757, 100.757, 106.932
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 CRISPR system Cmr subunit Cmr1-1 / Type III-B/RAMP module RAMP protein Cmr1-1


Mass: 39782.711 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 / Gene: cmr1-1, PF1130
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8U1S5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.94 Å3/Da / Density % sol: 68.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM bicine/Trizma base pH 6.0, 10% PEG 8000, 20% ethylene glycol, 20 mM each of sodium DL- alanine, sodium L-gutamate, gylcine, DL-lysine HCl, DL-serine and either 3% DMSO or 3% D-sorbitol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.037 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 33393 / % possible obs: 99.8 % / Redundancy: 19.4 % / Net I/σ(I): 18.2
Reflection shellResolution: 2.701→2.798 Å / Redundancy: 17.6 % / Mean I/σ(I) obs: 1.3 / % possible all: 97.88

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1678)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.7→45.589 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2195 1677 5.02 %
Rwork0.1882 --
obs0.1899 33393 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→45.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2645 0 0 28 2673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032711
X-RAY DIFFRACTIONf_angle_d0.693663
X-RAY DIFFRACTIONf_dihedral_angle_d14.05995
X-RAY DIFFRACTIONf_chiral_restr0.027398
X-RAY DIFFRACTIONf_plane_restr0.003460
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.77950.34811410.30632677X-RAY DIFFRACTION100
2.7795-2.86920.31911430.28812652X-RAY DIFFRACTION100
2.8692-2.97170.33391390.28672636X-RAY DIFFRACTION100
2.9717-3.09060.26811410.24272605X-RAY DIFFRACTION100
3.0906-3.23130.27731410.21482666X-RAY DIFFRACTION100
3.2313-3.40160.28741390.21492606X-RAY DIFFRACTION100
3.4016-3.61460.27321430.2032659X-RAY DIFFRACTION100
3.6146-3.89360.23231410.17912629X-RAY DIFFRACTION100
3.8936-4.28510.19991370.16922650X-RAY DIFFRACTION100
4.2851-4.90460.15041340.15212642X-RAY DIFFRACTION100
4.9046-6.17680.18041430.17642648X-RAY DIFFRACTION100
6.1768-45.59510.22091350.1812646X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 13.9224 Å / Origin y: 49.6218 Å / Origin z: 16.5057 Å
111213212223313233
T0.6798 Å20.0373 Å20.0612 Å2-0.6644 Å20.0476 Å2--0.6714 Å2
L0.957 °2-0.4712 °2-0.0167 °2-1.1255 °20.3935 °2--0.9101 °2
S-0.0811 Å °-0.0472 Å °-0.025 Å °0.1429 Å °0.1558 Å °-0.0107 Å °0.0444 Å °-0.033 Å °0.0013 Å °
Refinement TLS groupSelection details: all

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