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- PDB-4w8w: Crystal structure of oligomeric Cmr4 from Pyrococcus furiosus -

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Basic information

Entry
Database: PDB / ID: 4w8w
TitleCrystal structure of oligomeric Cmr4 from Pyrococcus furiosus
ComponentsCRISPR system Cmr subunit Cmr4
KeywordsHYDROLASE / Cmr4 / CMR complex / oligomeric / CRIPSR
Function / homologyCRISPR-associated RAMP Cmr4 / CRISPR type III-associated protein / RAMP superfamily / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / cytoplasm / CRISPR system Cmr endoribonuclease Cmr4
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.803 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 Cmr4
B: CRISPR system Cmr subunit Cmr4
C: CRISPR system Cmr subunit Cmr4
D: CRISPR system Cmr subunit Cmr4


Theoretical massNumber of molelcules
Total (without water)138,8434
Polymers138,8434
Non-polymers00
Water1,47782
1
A: CRISPR system Cmr subunit Cmr4


Theoretical massNumber of molelcules
Total (without water)34,7111
Polymers34,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CRISPR system Cmr subunit Cmr4


Theoretical massNumber of molelcules
Total (without water)34,7111
Polymers34,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CRISPR system Cmr subunit Cmr4


Theoretical massNumber of molelcules
Total (without water)34,7111
Polymers34,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CRISPR system Cmr subunit Cmr4


Theoretical massNumber of molelcules
Total (without water)34,7111
Polymers34,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.707, 129.509, 195.943
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
CRISPR system Cmr subunit Cmr4 / CRISPR type III-B/RAMP module RAMP protein Cmr4


Mass: 34710.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: cmr4, PF1126
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8U1S9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.91 Å3/Da / Density % sol: 57.75 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 30% Jeffamine M-600 and 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→49.38 Å / Num. obs: 76539 / % possible obs: 99.86 % / Redundancy: 6.5 % / Net I/σ(I): 12.61
Reflection shellResolution: 2.803→2.903 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.22 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1678)refinement
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.803→49.375 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.16 / Phase error: 26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3808 4.98 %random selection
Rwork0.1965 ---
obs0.1982 76539 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.803→49.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7942 0 0 82 8024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038065
X-RAY DIFFRACTIONf_angle_d0.62510901
X-RAY DIFFRACTIONf_dihedral_angle_d13.033021
X-RAY DIFFRACTIONf_chiral_restr0.0241298
X-RAY DIFFRACTIONf_plane_restr0.0031373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8028-2.83830.37121360.35542542X-RAY DIFFRACTION95
2.8383-2.87560.31981440.33892711X-RAY DIFFRACTION100
2.8756-2.9150.36341340.32682676X-RAY DIFFRACTION100
2.915-2.95670.37991380.32672710X-RAY DIFFRACTION100
2.9567-3.00080.32621430.33122721X-RAY DIFFRACTION100
3.0008-3.04770.38321350.31322684X-RAY DIFFRACTION100
3.0477-3.09760.3681390.29372679X-RAY DIFFRACTION100
3.0976-3.1510.29261490.282736X-RAY DIFFRACTION100
3.151-3.20830.3181430.2572733X-RAY DIFFRACTION100
3.2083-3.270.31711350.25652665X-RAY DIFFRACTION100
3.27-3.33670.27021430.24892717X-RAY DIFFRACTION100
3.3367-3.40930.25971420.2352662X-RAY DIFFRACTION100
3.4093-3.48860.28091440.2242717X-RAY DIFFRACTION100
3.4886-3.57580.26881500.21392692X-RAY DIFFRACTION100
3.5758-3.67240.28661390.21382690X-RAY DIFFRACTION100
3.6724-3.78050.24981380.20252734X-RAY DIFFRACTION100
3.7805-3.90240.22811400.18562677X-RAY DIFFRACTION100
3.9024-4.04190.22231470.17482724X-RAY DIFFRACTION100
4.0419-4.20360.20561420.15492689X-RAY DIFFRACTION100
4.2036-4.39480.16181370.14392685X-RAY DIFFRACTION100
4.3948-4.62640.14961480.12832695X-RAY DIFFRACTION100
4.6264-4.9160.1731400.14022725X-RAY DIFFRACTION100
4.916-5.29510.16971510.15222697X-RAY DIFFRACTION100
5.2951-5.82720.21071390.16762701X-RAY DIFFRACTION100
5.8272-6.66870.23591370.18732691X-RAY DIFFRACTION100
6.6687-8.39510.21251360.17232694X-RAY DIFFRACTION99
8.3951-49.38230.17021390.17042684X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -10.0584 Å / Origin y: -11.0708 Å / Origin z: 7.8916 Å
111213212223313233
T0.1392 Å2-0.0038 Å20.0203 Å2-0.1571 Å2-0.0229 Å2--0.1849 Å2
L-0.0596 °20.0118 °20.0193 °2-0.1312 °20.0593 °2--0.8496 °2
S0.0709 Å °-0.005 Å °0.0221 Å °-0.0001 Å °0.0953 Å °0.0124 Å °0.0025 Å °0.0223 Å °-0 Å °
Refinement TLS groupSelection details: all

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