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- PDB-2xlj: Crystal structure of the Csy4-crRNA complex, hexagonal form -

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Basic information

Entry
Database: PDB / ID: 2xlj
TitleCrystal structure of the Csy4-crRNA complex, hexagonal form
Components
  • 5'-R(*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP*CP*A*DG*C)-3'
  • CSY4 ENDORIBONUCLEASE
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / ENDORIBONUCLEASE / CRISPR
Function / homology
Function and homology information


maintenance of CRISPR repeat elements / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding
Similarity search - Function
Helicase, Ruva Protein; domain 3 - #890 / 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) / Helicase, Ruva Protein; domain 3 / Alpha-Beta Plaits / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / : / CRISPR-associated endonuclease Cas6/Csy4
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHaurwitz, R.E. / Jinek, M. / Wiedenheft, B. / Zhou, K. / Doudna, J.A.
CitationJournal: Science / Year: 2010
Title: Sequence- and Structure-Specific RNA Processing by a Crispr Endonuclease.
Authors: Haurwitz, R.E. / Jinek, M. / Wiedenheft, B. / Zhou, K. / Doudna, J.A.
History
DepositionJul 20, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CSY4 ENDORIBONUCLEASE
B: 5'-R(*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP*CP*A*DG*C)-3'


Theoretical massNumber of molelcules
Total (without water)26,9632
Polymers26,9632
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-11.1 kcal/mol
Surface area11910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.250, 39.250, 297.370
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein CSY4 ENDORIBONUCLEASE


Mass: 21866.002 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: UCBPP-PA14 / Plasmid: PHMGWA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 (DE3) / References: UniProt: A3KUJ4, UniProt: Q02MM2*PLUS
#2: RNA chain 5'-R(*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP*CP*A*DG*C)-3' / PA14 CRRNA HAIRPIN


Mass: 5097.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 2-DEOXY MODIFICATION AT G20 / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 22 TO CYS
Sequence detailsTHE SEQUENCE GSFT AT THE N-TERMINUS IS DERIVED FROM THE EXPRESSION VECTOR. THE DOWNSTREAM SEQUENCE ...THE SEQUENCE GSFT AT THE N-TERMINUS IS DERIVED FROM THE EXPRESSION VECTOR. THE DOWNSTREAM SEQUENCE MDHYLDIRLRPDPEFPPAQL IS NOT PRESENT IN THE GB YP_790814 ENTRY DUE TO MISANNOTATED METHIONINE START CODON. THE SEQUENCE CONFLICT STEMS A3KUJ4 CORRESPONDING TO A DIFFERENT P. AERUGINOSA STRAIN.

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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: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE
Crystal growpH: 4.6 / Details: 150 MM SODIUM ACETATE PH 4.6, 17% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11159
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11159 Å / Relative weight: 1
ReflectionResolution: 2.6→19.6 Å / Num. obs: 7798 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Biso Wilson estimate: 61.6 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 29.8
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XLI

2xli


Resolution: 2.6→19.625 Å / SU ML: 0.54 / σ(F): 2 / Phase error: 36.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 388 5 %
Rwork0.2485 --
obs0.2497 7798 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.886 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 102.4 Å2
Baniso -1Baniso -2Baniso -3
1-23.4079 Å20 Å2-0 Å2
2--23.4079 Å20 Å2
3----46.8159 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 321 0 5 1743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031811
X-RAY DIFFRACTIONf_angle_d0.6532522
X-RAY DIFFRACTIONf_dihedral_angle_d16.725721
X-RAY DIFFRACTIONf_chiral_restr0.038280
X-RAY DIFFRACTIONf_plane_restr0.003278
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6014-2.97670.3831280.33532452X-RAY DIFFRACTION99
2.9767-3.74610.24791290.23192471X-RAY DIFFRACTION99
3.7461-19.62550.25051310.23292487X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6605-0.7663-0.98686.1516-0.39157.221-0.10890.10070.00860.02920.1632-0.1274-0.11740.160700.67520.3621-0.05830.3561-0.12240.5142-17.33593.5159-22.9719
2-0.00240.0859-0.00550.1821-0.06340.0066-0.2482-0.30050.9019-0.15360.05730.9233-0.8926-2.3294-0.00121.0321-0.3599-0.29371.60780.02910.9171-34.5452-2.4335-52.0052
31.2145-0.0528-0.19150.7593-0.96971.21950.00220.357-0.14210.43430.1442-0.00331.3652-2.15120.0011.55-0.0866-0.1540.7367-0.16740.7621-24.393-3.3367-45.3922
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND NOT RESID 108:130
2X-RAY DIFFRACTION2CHAIN A AND RESID 108:130
3X-RAY DIFFRACTION3CHAIN B

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