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- PDB-4al5: Crystal structure of the Csy4-crRNA product complex -

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Basic information

Entry
Database: PDB / ID: 4al5
TitleCrystal structure of the Csy4-crRNA product complex
Components
  • 5'-R(*UP*UP*CP*AP*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP *GP*GP*CP*AP*GP*C)-3'
  • CSY4 ENDORIBONUCLEASE
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / 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
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
RNA / RNA (> 10) / CRISPR-associated endonuclease Cas6/Csy4
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHaurwitz, R.E. / Sternberg, S.H. / Doudna, J.A.
CitationJournal: Embo J. / Year: 2012
Title: Csy4 Relies on an Unusual Catalytic Dyad to Position and Cleave Crispr RNA.
Authors: Haurwitz, R.E. / Sternberg, S.H. / Doudna, J.A.
History
DepositionMar 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Other
Revision 1.2Dec 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_site
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_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: CSY4 ENDORIBONUCLEASE
B: 5'-R(*UP*UP*CP*AP*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP *GP*GP*CP*AP*GP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2883
Polymers28,1962
Non-polymers921
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-15.8 kcal/mol
Surface area11350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.790, 47.800, 86.570
Angle α, β, γ (deg.)90.00, 109.69, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2072-

HOH

21A-2074-

HOH

31A-2099-

HOH

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Components

#1: Protein CSY4 ENDORIBONUCLEASE


Mass: 21835.977 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: UCBPP-PA14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q02MM2
#2: RNA chain 5'-R(*UP*UP*CP*AP*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP *GP*GP*CP*AP*GP*C)-3' / CRRNA


Mass: 6359.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 22 TO CYS
Sequence detailsTHE DATABASE ENTRY IS MISSING THE N-TERMINAL 20 AMINO ACIDS BECAUSE THE START CODON IS INCORRECTLY ...THE DATABASE ENTRY IS MISSING THE N-TERMINAL 20 AMINO ACIDS BECAUSE THE START CODON IS INCORRECTLY ANNOTATED. ( THEREFORE THE DATABASE ENTRY IS ONLY 167 AMINO ACIDS IN LENGTH.) CRRNA REPEAT SEQUENCE DERIVED FROM CRISPR LOCUS LOCATED 2926520-2927393

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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: 2.14 Å3/Da / Density % sol: 47.17 % / Description: NONE
Crystal growpH: 5
Details: 22 % PEG4000, 120 MM SODIUM CITRATE PH 5.0, 50 MM MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2→81.51 Å / Num. obs: 15945 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 23.89 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.58
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.06 / % possible all: 99

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Processing

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

2xlk


Resolution: 2→81.508 Å / SU ML: 0.28 / σ(F): 2 / Phase error: 22.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 797 5 %
Rwork0.1829 --
obs0.1857 15934 99.69 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.346 Å2 / ksol: 0.438 e/Å3
Displacement parametersBiso mean: 33.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.4691 Å20 Å24.8929 Å2
2--0.6628 Å20 Å2
3----3.1319 Å2
Refinement stepCycle: LAST / Resolution: 2→81.508 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1455 348 6 128 1937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121891
X-RAY DIFFRACTIONf_angle_d1.3282649
X-RAY DIFFRACTIONf_dihedral_angle_d13.504744
X-RAY DIFFRACTIONf_chiral_restr0.119302
X-RAY DIFFRACTIONf_plane_restr0.007289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12530.26781400.20882477X-RAY DIFFRACTION100
2.1253-2.28940.26661320.20232523X-RAY DIFFRACTION100
2.2894-2.51980.27591270.19022508X-RAY DIFFRACTION100
2.5198-2.88450.28051310.18132522X-RAY DIFFRACTION100
2.8845-3.63420.23341340.162523X-RAY DIFFRACTION100
3.6342-81.57540.20151330.18492584X-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)
10.07420.0263-0.01750.07390.03040.0766-0.0880.07530.0202-0.02570.06010.05330.0254-0.0052-0.04680.0522-0.0136-0.01640.0507-0.00170.096710.68121.593128.39
20.01360.0057-0.00120.003-0.00040.00010.01120.0035-0.0257-0.0031-0.0163-0.01840.0095-0.01460.00060.47680.01630.0970.3563-0.10530.224920.795-15.1481.4079
30.0339-0.0093-0.01920.019-0.01270.03420.02270.0350.0052-0.091-0.0138-0.0110.03980.01930.02850.3278-0.08330.13970.4569-0.02680.1317.9045-5.66656.5232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID -1:104 OR RESID 139:187)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 105:138)
3X-RAY DIFFRACTION3CHAIN B

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