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- PDB-3ung: Structure of the Cmr2 subunit of the CRISPR RNA silencing complex -

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Basic information

Entry
Database: PDB / ID: 3ung
TitleStructure of the Cmr2 subunit of the CRISPR RNA silencing complex
ComponentsCmr2dHD
KeywordsUNKNOWN FUNCTION / Ferredoxin Fold / nucleotide-binding / Polymerase / Cmr complex
Function / homology
Function and homology information


defense response to virus / nucleotide binding / RNA binding / metal ion binding / cytoplasm
Similarity search - Function
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 Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster ...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 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 / : / Cas10/Cmr2, second palm 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / CRISPR system Cmr subunit Cmr2
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsCocozaki, A.I. / Ramia, N.F. / Shao, Y. / Hale, C.R. / Terns, R.M. / Terns, M.P. / Li, H.
CitationJournal: Structure / Year: 2012
Title: Structure of the Cmr2 Subunit of the CRISPR-Cas RNA Silencing Complex.
Authors: Cocozaki, A.I. / Ramia, N.F. / Shao, Y. / Hale, C.R. / Terns, R.M. / Terns, M.P. / Li, H.
History
DepositionNov 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Other
Revision 1.2Feb 4, 2015Group: Other
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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

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Assembly

Deposited unit
C: Cmr2dHD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7195
Polymers80,1461
Non-polymers5734
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.167, 85.070, 140.087
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 Cmr2dHD


Mass: 80146.406 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 215-871
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: ATCC 43587 / DSM 3638 / JCM 8422 / Vc1 / Gene: PF1129 / Plasmid: pET200D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8U1S6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.2M CaCl2, 28% PEG 400, 0.1M HEPES Sodium, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 303.15K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 12, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 35291 / Num. obs: 35291 / % possible obs: 90.7 % / Observed criterion σ(F): 5 / Observed criterion σ(I): 5
Reflection shellResolution: 2.3→2.34 Å / % possible all: 51.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.31→29.614 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 32.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2639 1778 5.69 %
Rwork0.203 --
obs0.2064 31257 79.94 %
all-35291 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.553 Å2 / ksol: 0.343 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.3341 Å20 Å2-0 Å2
2--6.4372 Å20 Å2
3----16.7713 Å2
Refinement stepCycle: LAST / Resolution: 2.31→29.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 30 35 4534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154796
X-RAY DIFFRACTIONf_angle_d1.2556196
X-RAY DIFFRACTIONf_dihedral_angle_d16.3651732
X-RAY DIFFRACTIONf_chiral_restr0.088691
X-RAY DIFFRACTIONf_plane_restr0.005764
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.31-2.37210.3364480.3068966X-RAY DIFFRACTION34
2.3721-2.44180.3621810.27481333X-RAY DIFFRACTION47
2.4418-2.52060.38451050.27251678X-RAY DIFFRACTION60
2.5206-2.61060.33671220.26581961X-RAY DIFFRACTION71
2.6106-2.71510.31561420.27422157X-RAY DIFFRACTION77
2.7151-2.83860.37671380.26482286X-RAY DIFFRACTION82
2.8386-2.98810.36951420.27712405X-RAY DIFFRACTION85
2.9881-3.17510.30011530.25132588X-RAY DIFFRACTION92
3.1751-3.41990.26361640.23622703X-RAY DIFFRACTION95
3.4199-3.76350.24221660.18842750X-RAY DIFFRACTION97
3.7635-4.30660.22091670.1612835X-RAY DIFFRACTION98
4.3066-5.42050.20771720.14732861X-RAY DIFFRACTION100
5.4205-29.61610.27311780.21192956X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 8.082 Å / Origin y: 16.8858 Å / Origin z: 12.6916 Å
111213212223313233
T0.1132 Å2-0.0199 Å2-0.0157 Å2-0.1726 Å20.0586 Å2--0.1655 Å2
L2.0864 °20.2359 °2-0.9673 °2-1.2901 °20.5792 °2--2.2229 °2
S-0.0415 Å °-0.1536 Å °-0.0851 Å °0.0604 Å °-0.0582 Å °-0.2432 Å °0.0658 Å °0.134 Å °-0.1035 Å °
Refinement TLS groupSelection details: all

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