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- PDB-3w2v: Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP -

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Basic information

Entry
Database: PDB / ID: 3w2v
TitleCrystal structure of the Cmr2dHD-Cmr3 subcomplex bound to 3'-AMP
Components
  • CRISPR system Cmr subunit Cmr2
  • CRISPR system Cmr subunit Cmr3
KeywordsIMMUNE SYSTEM / ferredoxin-like fold
Function / homology
Function and homology information


defense response to virus / nucleotide binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
Immunoglobulin-like - #4350 / Carboxypeptidase Inhibitor; Chain A - #70 / CRISPR-Cas system, Cmr2 subunit, D2 domain, helical bundle / CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / : / : / CRISPR RNA silencing complex Cmr2 subunit, first helical domain / CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain / CRISPR-associated protein, TM1793 ...Immunoglobulin-like - #4350 / Carboxypeptidase Inhibitor; Chain A - #70 / CRISPR-Cas system, Cmr2 subunit, D2 domain, helical bundle / CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / : / : / CRISPR RNA silencing complex Cmr2 subunit, first helical domain / CRISPR RNA silencing complex Cmr2 subunit, Zn-binding domain / CRISPR-associated protein, TM1793 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / Carboxypeptidase Inhibitor; Chain A / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / : / CRISPR RNA silencing complex Cmr2 subunit, second helical domain / GGDEF domain profile. / GGDEF domain / Reverse transcriptase/Diguanylate cyclase domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Arc Repressor Mutant, subunit A / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Up-down Bundle / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-3AM / CRISPR system Cmr subunit Cmr2 / CRISPR system Cmr subunit Cmr3
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNumata, T. / Osawa, T.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal Structure of the Cmr2-Cmr3 Subcomplex in the CRISPR-Cas RNA Silencing Effector Complex.
Authors: Osawa, T. / Inanaga, H. / Numata, T.
History
DepositionDec 6, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR system Cmr subunit Cmr2
B: CRISPR system Cmr subunit Cmr3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,0054
Polymers114,5932
Non-polymers4132
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-12 kcal/mol
Surface area38570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.940, 136.669, 191.973
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CRISPR system Cmr subunit Cmr2 / CRISPR-associated protein Cas10/Cmr2 / subtype III-B


Mass: 78226.383 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 216-871
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: cmr2, PF1129 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q8U1S6
#2: Protein CRISPR system Cmr subunit Cmr3 / CRISPR type III-B/RAMP module-associated protein Cmr3


Mass: 36366.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / Gene: cmr3, PF1128 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL / References: UniProt: Q8U1S7
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-3AM / [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate / 3'-AMP


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12.5-15% 2-propanaol, 18mM MgCl2, 45mM MES (pH 6.0), 20mM ammonium acetate, 10mM sodium acetate, 3% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 22, 2012
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 42206 / % possible obs: 99.7 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.063 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UNG

3ung


Resolution: 2.6→41.73 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 4088877.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2077 4.9 %RANDOM
Rwork0.215 ---
obs0.215 42206 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.7939 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 63.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.2 Å20 Å20 Å2
2--3.2 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7046 0 24 26 7096
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.532
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 343 5 %
Rwork0.277 6547 -
obs--98.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION33AM-2.param3AM-2.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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