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- PDB-4wnz: Crystal structure of Pyrococcus furiosus Cmr4 (Cas7) -

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Basic information

Entry
Database: PDB / ID: 4wnz
TitleCrystal structure of Pyrococcus furiosus Cmr4 (Cas7)
ComponentsCRISPR system Cmr subunit Cmr4
KeywordsHYDROLASE / Nuclease / RAMP domain / CRISPR-Cas system / CMR cmplex
Function / homologyCRISPR-associated RAMP Cmr4 / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / cytoplasm / CRISPR system Cmr endoribonuclease Cmr4
Function and homology information
Biological speciesPyrococcus furiosus DSM 3638 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsZhu, X. / Ye, K.
Funding support China, 3items
OrganizationGrant numberCountry
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08010203 China
National Natural Science Foundation of China31325007 China
National Basic Research Program of China, Ministry of Science and Technology of China2010CB835402 China
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Cmr4 is the slicer in the RNA-targeting Cmr CRISPR complex
Authors: Zhu, X. / Ye, K.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 4, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / refine_hist / struct_keywords
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text

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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


Theoretical massNumber of molelcules
Total (without water)66,9972
Polymers66,9972
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-3 kcal/mol
Surface area20730 Å2
Unit cell
Length a, b, c (Å)63.997, 63.997, 195.344
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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


Mass: 33498.434 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus DSM 3638 (archaea) / Gene: cmr4 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8U1S9

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium citrate, 7% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 19448 / % possible obs: 98.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 70.45 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 13.7
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 2.4 / % possible all: 93.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: SAD / Resolution: 2.8→19.817 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1929 10.07 %Random selection
Rwork0.197 ---
obs0.2002 19149 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3728 0 0 0 3728
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033782
X-RAY DIFFRACTIONf_angle_d0.665100
X-RAY DIFFRACTIONf_dihedral_angle_d13.091426
X-RAY DIFFRACTIONf_chiral_restr0.026612
X-RAY DIFFRACTIONf_plane_restr0.003632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7948-2.86450.3327990.27111202X-RAY DIFFRACTION95
2.8645-2.94170.30351970.25851158X-RAY DIFFRACTION99
2.9417-3.0280.2742980.25651300X-RAY DIFFRACTION99
3.028-3.12540.26461720.25071194X-RAY DIFFRACTION100
3.1254-3.23660.27391210.23271250X-RAY DIFFRACTION100
3.2366-3.36560.2329990.221292X-RAY DIFFRACTION99
3.3656-3.5180.26941990.2211148X-RAY DIFFRACTION100
3.518-3.70230.2403990.21081266X-RAY DIFFRACTION100
3.7023-3.93260.24721910.21021198X-RAY DIFFRACTION100
3.9326-4.23350.2207970.19071280X-RAY DIFFRACTION100
4.2335-4.65450.1814960.15671270X-RAY DIFFRACTION99
4.6545-5.31670.21021900.16971212X-RAY DIFFRACTION100
5.3167-6.6560.2319940.1991263X-RAY DIFFRACTION99
6.656-19.81720.19451770.17751187X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 6.4894 Å / Origin y: -46.6875 Å / Origin z: -0.5374 Å
111213212223313233
T0.4074 Å20.0175 Å2-0.0044 Å2-0.4086 Å20.0254 Å2--0.5053 Å2
L1.1715 °20.2529 °2-1.3869 °2-1.0616 °2-0.2204 °2--4.1017 °2
S0.0892 Å °-0.189 Å °0.0011 Å °-0.2375 Å °0.1247 Å °0.0789 Å °-0.2302 Å °-0.0975 Å °-0.0336 Å °
Refinement TLS groupSelection details: all

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