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- PDB-3w2w: Crystal structure of the Cmr2dHD-Cmr3 subcomplex bound to ATP -

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Basic information

Entry
Database: PDB / ID: 3w2w
TitleCrystal structure of the Cmr2dHD-Cmr3 subcomplex bound to ATP
Components(CRISPR system Cmr subunit ...) x 2
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
ADENOSINE-5'-TRIPHOSPHATE / CRISPR system Cmr subunit Cmr2 / CRISPR system Cmr subunit Cmr3
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

Downloads & links

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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)115,7217
Polymers114,5932
Non-polymers1,1285
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-33 kcal/mol
Surface area41980 Å2
MethodPISA
2
A: CRISPR system Cmr subunit Cmr2
B: CRISPR system Cmr subunit Cmr3
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)231,44214
Polymers229,1864
Non-polymers2,25710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area21420 Å2
ΔGint-116 kcal/mol
Surface area73260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.579, 135.804, 191.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

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CRISPR system Cmr subunit ... , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 66 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.94 Å3/Da / Density % sol: 58.1 %
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% PEG4000, 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: 2.5→50 Å / Num. obs: 46626 / % possible obs: 99.8 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.063 / % possible all: 99.8

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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: 3W2V

3w2v


Resolution: 2.5→46.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4340095.78 / 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
Rfree0.246 2323 5 %RANDOM
Rwork0.211 ---
obs0.211 46626 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6874 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 54.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.33 Å20 Å20 Å2
2---1.79 Å20 Å2
3----1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7373 0 65 61 7499
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_d22.8
X-RAY DIFFRACTIONc_improper_angle_d2.26
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.382
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.152.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 357 4.8 %
Rwork0.254 7096 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3ATP.paramATP.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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