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- PDB-2xlk: Crystal structure of the Csy4-crRNA complex, orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 2xlk
TitleCrystal structure of the Csy4-crRNA complex, orthorhombic 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
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: 1.805 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 21, 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: CSY4 ENDORIBONUCLEASE
C: 5'-R(*CP*UP*GP*CP*CP*GP*UP*AP*UP*AP*GP*GP*CP*A*DG*C)-3'
D: 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)53,9264
Polymers53,9264
Non-polymers00
Water7,440413
1
B: CSY4 ENDORIBONUCLEASE
D: 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-12.7 kcal/mol
Surface area11550 Å2
MethodPISA
2
A: CSY4 ENDORIBONUCLEASE
C: 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
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-12.4 kcal/mol
Surface area12220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.060, 78.910, 145.940
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 CSY4 ENDORIBONUCLEASE


Mass: 21866.002 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Details: 2-DEOXY MODIFICATION AT G20 / Source: (synth.) PSEUDOMONAS AERUGINOSA (bacteria)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 22 TO CYS ENGINEERED RESIDUE IN CHAIN B, 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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: NONE
Crystal growpH: 4.6 / Details: 160 MM SODIUM ACETATE PH 4.6, 18% (W/V) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.99992
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99992 Å / Relative weight: 1
ReflectionResolution: 1.8→69.4 Å / Num. obs: 43284 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 19.8 % / Biso Wilson estimate: 21.95 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 31.1
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.1 / % possible all: 91

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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: 1.805→69.413 Å / SU ML: 0.21 / σ(F): 2 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 2164 5 %
Rwork0.1844 --
obs0.186 43284 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.571 Å2 / ksol: 0.341 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.3678 Å20 Å2-0 Å2
2--4.1419 Å20 Å2
3----3.7742 Å2
Refinement stepCycle: LAST / Resolution: 1.805→69.413 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 642 0 413 4030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063791
X-RAY DIFFRACTIONf_angle_d1.0865275
X-RAY DIFFRACTIONf_dihedral_angle_d14.9891534
X-RAY DIFFRACTIONf_chiral_restr0.07585
X-RAY DIFFRACTIONf_plane_restr0.005587
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.805-1.8470.30041330.23452514X-RAY DIFFRACTION93
1.847-1.89320.2571420.21032704X-RAY DIFFRACTION100
1.8932-1.94440.20321410.18722692X-RAY DIFFRACTION100
1.9444-2.00160.24081440.18332748X-RAY DIFFRACTION100
2.0016-2.06620.20911410.18612684X-RAY DIFFRACTION100
2.0662-2.14010.23591430.17662717X-RAY DIFFRACTION100
2.1401-2.22570.20281450.18212748X-RAY DIFFRACTION100
2.2257-2.3270.22341440.17872726X-RAY DIFFRACTION100
2.327-2.44970.24081430.19772732X-RAY DIFFRACTION100
2.4497-2.60320.26391450.19132748X-RAY DIFFRACTION100
2.6032-2.80420.23651450.19892756X-RAY DIFFRACTION100
2.8042-3.08640.22631460.19292775X-RAY DIFFRACTION100
3.0864-3.5330.1931460.17052782X-RAY DIFFRACTION100
3.533-4.45110.18631500.15372832X-RAY DIFFRACTION100
4.4511-69.46430.19321560.17962962X-RAY DIFFRACTION100
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)
10.2950.21490.2070.46880.01510.57450.0455-0.11780.024-0.0489-0.0801-0.0142-0.02930.06330.00020.06660.0176-0.00070.1851-0.02090.120114.331926.268730.9088
20.00330.01180.0240.0828-0.05580.03360.06050.04420.04410.0228-0.286-0.24470.1516-0.026100.3148-0.0791-0.01380.17240.03310.203519.854321.436864.0839
30.2761-0.032-0.07861.05480.22480.5517-0.0753-0.0427-0.0054-0.02340.0948-0.01060.082-0.02410.15130.06660.01170.0020.05830.00480.10173.86658.957310.369
40.0465-0.0164-0.0054-0.01470.00550.03360.01960.0011-0.2995-0.5240.2156-0.11260.23320.34060.00540.48560.04540.11080.1467-0.09220.213218.7493-12.196-13.9495
50.1509-0.02540.12170.03580.04080.0663-0.07720.23590.05910.15110.0584-0.00780.1309-0.025100.28910.0504-0.00290.28710.01120.159914.118328.181855.4057
60.44320.2897-0.28310.2869-0.07180.24740.21330.00280.10050.6708-0.0126-0.0537-0.0442-0.03110.09120.4622-0.0142-0.09760.1211-0.02430.1162-8.457941.02349.978
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND NOT RESID 109:139
2X-RAY DIFFRACTION2CHAIN A AND RESID 109:138
3X-RAY DIFFRACTION3CHAIN B AND NOT RESID 109:135
4X-RAY DIFFRACTION4CHAIN B AND RESID 109:135
5X-RAY DIFFRACTION5CHAIN C
6X-RAY DIFFRACTION6CHAIN D

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