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- PDB-5o6u: Structure of the Cascade-I-Fv R-loop complex from Shewanella putr... -

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Basic information

Entry
Database: PDB / ID: 5o6u
TitleStructure of the Cascade-I-Fv R-loop complex from Shewanella putrefaciens
Components
  • (Uncharacterized ...) x 2
  • CRISPR-associated protein, Csy4 family
  • crRNA
  • non-target DNA
  • target DNA
KeywordsANTIVIRAL PROTEIN / RNA SURVEILLANCE / ADAPTIVE IMMUNITY / CRISPR / CASCADE
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity
Similarity search - Function
Cas5fv helical domain / : / : / Cas5fv helical domain / CRISPR-associated endoribonuclease Cas6/Csy4 / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST / CRISPR-associated endoribonuclease Cas6/Csy4, subtype I-F/YPEST superfamily / CRISPR-associated protein (Cas_Csy4) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Uncharacterized protein / Cas5fv helical domain-containing protein / CRISPR-associated protein, Csy4 family
Similarity search - Component
Biological speciesShewanella putrefaciens CN-32 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsPausch, P. / Altegoer, F. / Bange, G.
CitationJournal: Mol. Cell / Year: 2017
Title: Structural Variation of Type I-F CRISPR RNA Guided DNA Surveillance.
Authors: Pausch, P. / Muller-Esparza, H. / Gleditzsch, D. / Altegoer, F. / Randau, L. / Bange, G.
History
DepositionJun 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_seq_map_depositor_info ...pdbx_data_processing_status / pdbx_seq_map_depositor_info / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3May 8, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: crRNA
B: CRISPR-associated protein, Csy4 family
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein
H: non-target DNA
I: target DNA


Theoretical massNumber of molelcules
Total (without water)193,8368
Polymers193,8368
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35150 Å2
ΔGint-150 kcal/mol
Surface area65840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.316, 143.316, 172.698
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Uncharacterized ... , 2 types, 4 molecules CDEF

#3: Protein Uncharacterized protein


Mass: 35602.055 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_1821 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G1
#4: Protein Uncharacterized protein


Mass: 37904.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_1822 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G2

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DNA chain , 2 types, 2 molecules HI

#5: DNA chain non-target DNA


Mass: 6310.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#6: DNA chain target DNA


Mass: 8485.428 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)

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RNA chain / Protein , 2 types, 2 molecules AB

#1: RNA chain crRNA


Mass: 13756.292 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein CRISPR-associated protein, Csy4 family


Mass: 20573.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella putrefaciens CN-32 (bacteria)
Gene: Sputcn32_1823 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4Y6G3

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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: 54.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 22.5 % w/v PEG4000, 15 % v/v glycerol, 153 mM ammonium acetate and 85 mM sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.991 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991 Å / Relative weight: 1
ReflectionResolution: 3.25→47.66 Å / Num. obs: 32784 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.168 / Net I/σ(I): 11.66
Reflection shellResolution: 3.25→3.36 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1.8 / CC1/2: 0.85 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.25→46.911 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.94
RfactorNum. reflection% reflection
Rfree0.2856 1587 4.85 %
Rwork0.2523 --
obs0.254 32783 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.25→46.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11250 1881 0 0 13131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313571
X-RAY DIFFRACTIONf_angle_d0.82718710
X-RAY DIFFRACTIONf_dihedral_angle_d16.915261
X-RAY DIFFRACTIONf_chiral_restr0.0332105
X-RAY DIFFRACTIONf_plane_restr0.0032083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.30080.36711100.3642686X-RAY DIFFRACTION100
3.3008-3.35490.42311170.35162745X-RAY DIFFRACTION100
3.3549-3.41280.37911080.36432737X-RAY DIFFRACTION100
3.4128-3.47480.39151640.33842618X-RAY DIFFRACTION100
3.4748-3.54160.35442020.32942621X-RAY DIFFRACTION100
3.5416-3.61390.41121580.30552698X-RAY DIFFRACTION100
3.6139-3.69240.34671220.30562712X-RAY DIFFRACTION100
3.6924-3.77830.35841700.28922655X-RAY DIFFRACTION100
3.7783-3.87270.38091440.28732692X-RAY DIFFRACTION99
3.8727-3.97740.27731400.28852699X-RAY DIFFRACTION100
3.9774-4.09430.31231220.252685X-RAY DIFFRACTION100
4.0943-4.22640.26451130.24252724X-RAY DIFFRACTION100
4.2264-4.37740.24541400.2322697X-RAY DIFFRACTION100
4.3774-4.55250.2811560.22082666X-RAY DIFFRACTION100
4.5525-4.75950.24171440.22112692X-RAY DIFFRACTION100
4.7595-5.01020.28671140.22672707X-RAY DIFFRACTION100
5.0102-5.32370.23711180.23022751X-RAY DIFFRACTION100
5.3237-5.7340.30591660.2492673X-RAY DIFFRACTION100
5.734-6.30980.26421020.26252726X-RAY DIFFRACTION100
6.3098-7.220.3641000.2442749X-RAY DIFFRACTION100
7.22-9.08570.23651600.23122663X-RAY DIFFRACTION100
9.0857-46.9160.22471550.21422690X-RAY DIFFRACTION100

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