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- PDB-4w8x: Crystal Structure of Cmr1 from Pyrococcus furiosus bound to a nuc... -

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Basic information

Entry
Database: PDB / ID: 4w8x
TitleCrystal Structure of Cmr1 from Pyrococcus furiosus bound to a nucleotide
ComponentsCRISPR system Cmr subunit Cmr1-1
KeywordsRNA BINDING PROTEIN / Cmr1 / CMR complex / nucleotide-bound / CRISPR
Function / homology
Function and homology information


defense response to virus / RNA binding / cytoplasm
Similarity search - Function
: / Cmr1-like, C-terminal / CRISPR-associated protein TM1795 / CRISPR type III-associated protein / RAMP superfamily
Similarity search - Domain/homology
GUANOSINE-3'-MONOPHOSPHATE / PHOSPHATE ION / CRISPR system Cmr subunit Cmr1-1
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBenda, C. / Ebert, J. / Baumgaertner, M. / Conti, E.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationFOR1680 Germany
European Research Council294371 Germany
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 2.0Jan 10, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_nonpoly_scheme.auth_seq_num / _struct_site_gen.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR system Cmr subunit Cmr1-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2413
Polymers39,7831
Non-polymers4582
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-6 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.057, 101.057, 107.947
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-3GP / GUANOSINE-3'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 4 Å3/Da / Density % sol: 69.25 %
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, 3% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.91→87.5 Å / Num. obs: 25373 / % possible obs: 94.94 % / Redundancy: 9.4 % / Net I/σ(I): 15.18
Reflection shellResolution: 2.91→3.07 Å / Redundancy: 9.4 % / Mean I/σ(I) obs: 1.6 / % possible all: 89.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1678)refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4w8z

4w8z


Resolution: 3→87.518 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.27 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 1213 5.13 %
Rwork0.1697 --
obs0.1716 23624 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→87.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2646 0 29 15 2690
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012742
X-RAY DIFFRACTIONf_angle_d1.2153710
X-RAY DIFFRACTIONf_dihedral_angle_d16.0641006
X-RAY DIFFRACTIONf_chiral_restr0.047402
X-RAY DIFFRACTIONf_plane_restr0.006461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.12030.29721380.29172631X-RAY DIFFRACTION100
3.1203-3.26230.3421400.25682624X-RAY DIFFRACTION100
3.2623-3.43430.31831310.23362419X-RAY DIFFRACTION95
3.4343-3.64950.26951220.19642275X-RAY DIFFRACTION88
3.6495-3.93120.22921090.18552047X-RAY DIFFRACTION79
3.9312-4.32680.18031410.14252611X-RAY DIFFRACTION100
4.3268-4.95290.17051420.12462598X-RAY DIFFRACTION100
4.9529-6.23990.15411400.16172608X-RAY DIFFRACTION100
6.2399-87.55510.20241500.16062598X-RAY DIFFRACTION100

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