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- PDB-4c9d: Cas6 (TTHB231) product complex -

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Basic information

Entry
Database: PDB / ID: 4c9d
TitleCas6 (TTHB231) product complex
Components
  • CAS6B
  • R3 REPEAT RNA CLEAVAGE PRODUCT
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / CRISPR / RNA PROCESSING RIBONUCLEASE
Function / homology
Function and homology information


defense response to virus / endonuclease activity
Similarity search - Function
: / CRISPR Cas6 N-terminal domain / CRISPR-associated protein Cas6, N-terminal domain superfamily / CRISPR-associated protein Cas6, C-terminal / CRISPR-associated endoribonuclease Cas6 / Alpha-Beta Plaits - #1890 / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Uncharacterized protein
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsJinek, M. / Niewoehner, O. / Doudna, J.A.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases.
Authors: Niewoehner, O. / Jinek, M. / Doudna, J.A.
History
DepositionOct 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 1, 2017Group: Database references
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_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: CAS6B
B: CAS6B
C: R3 REPEAT RNA CLEAVAGE PRODUCT
D: R3 REPEAT RNA CLEAVAGE PRODUCT


Theoretical massNumber of molelcules
Total (without water)77,2984
Polymers77,2984
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-40.4 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.220, 75.220, 308.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CAS6B


Mass: 29270.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS HB8 (bacteria) / Plasmid: PEC-K-MBP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: Q53VU8
#2: RNA chain R3 REPEAT RNA CLEAVAGE PRODUCT


Mass: 9378.525 Da / Num. of mol.: 2 / Fragment: REPEAT STEM-LOOP / Source method: obtained synthetically / Details: R3 REPEAT RNA CLEAVAGE PRODUCT / Source: (synth.) THERMUS THERMOPHILUS HB8 (bacteria)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL GAAS TAG DERIVED FROM EXPRESSION PLASMID

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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: 3.22 Å3/Da / Density % sol: 61.8 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1M TRIS (PH 8.5), 13% (W/V) PEG 65 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.99994
DetectorType: ADSC / Detector: CCD / Date: Apr 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99994 Å / Relative weight: 1
ReflectionResolution: 3→73.08 Å / Num. obs: 18676 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 57.15 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.6
Reflection shellResolution: 3→3.08 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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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 4C98

4c98


Resolution: 3→73.083 Å / SU ML: 0.38 / σ(F): 1.99 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2907 935 5 %
Rwork0.2436 --
obs0.246 18676 99.71 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.413 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 58.8 Å2
Baniso -1Baniso -2Baniso -3
1-10.8857 Å20 Å20 Å2
2--10.8857 Å20 Å2
3----21.7715 Å2
Refinement stepCycle: LAST / Resolution: 3→73.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4062 548 0 15 4625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054792
X-RAY DIFFRACTIONf_angle_d0.9426639
X-RAY DIFFRACTIONf_dihedral_angle_d15.9211855
X-RAY DIFFRACTIONf_chiral_restr0.048743
X-RAY DIFFRACTIONf_plane_restr0.005766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.15830.36311290.32962446X-RAY DIFFRACTION100
3.1583-3.35610.31721300.29332473X-RAY DIFFRACTION100
3.3561-3.61530.31981320.27682495X-RAY DIFFRACTION100
3.6153-3.97910.30161320.24712508X-RAY DIFFRACTION100
3.9791-4.55480.2991320.20912521X-RAY DIFFRACTION100
4.5548-5.73820.25361350.20112573X-RAY DIFFRACTION100
5.7382-73.10440.26251450.24232725X-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)
10.46470.2923-0.26990.37320.05830.4035-0.0635-0.18530.0292-0.14080.0747-0.1089-0.35950.31350.00480.3416-0.0813-0.01770.3379-0.03280.257744.640276.8736315.471
20.10210.0458-0.01620.21160.08410.05130.03540.1341-0.1015-0.12820.1363-0.11930.08110.02730.12520.64770.0307-0.12630.6399-0.15620.34943.724575.1505304.2045
30.24-0.13060.02860.0849-0.03750.0392-0.0802-0.1049-0.3337-0.07810.0277-0.0895-0.08180.12310.00160.4945-0.03160.050.455-0.05650.308149.967270.2372312.115
40.5975-0.02170.30570.4683-0.32860.5333-0.09060.03460.13440.10650.0986-0.12360.0187-0.3586-0.22390.1767-0.03360.02680.4344-0.02240.204829.986969.5339328.3637
50.0288-0.0827-0.00160.33430.01850.00040.0370.2249-0.1584-0.03730.06580.3207-0.0649-0.16550.10640.2846-0.069-0.05860.66560.11420.429623.365370.3305320.9707
60.23380.2794-0.06121.04390.26040.278-0.0353-0.1307-0.08050.08060.2799-0.3253-0.05530.08320.75730.0931-0.0974-0.00750.5347-0.0490.170129.100668.1236332.4504
70.09870.0842-0.0760.079-0.03950.3246-0.09910.2474-0.1063-0.13210.04870.1020.0891-0.3813-0.06740.1438-0.11540.00790.4776-0.01810.295830.9266.5847322.8149
80.27280.1362-0.10560.1056-0.07970.0575-0.01720.06120.1045-0.0149-0.08160.25070.1011-0.0945-0.00710.2832-0.009-0.01760.4725-0.01760.27234.400355.4291368.1208
90.0038-0.0057-0.00630.0085-0.01060.01860.08120.0170.14470.0101-0.18980.08580.0429-0.078-0.00280.147-0.01470.05980.3674-0.10660.325924.212653.2771368.9752
100.057-0.04340.10410.4193-0.00280.4327-0.0483-0.02250.07260.05840.0010.08630.123-0.37430.10080.26870.03310.0930.6775-0.06040.379827.221859.2237365.572
111.2355-0.7045-0.47910.64640.2850.2179-0.1603-0.1898-0.32480.18910.06030.19430.22740.01780.26990.1820.03470.06670.6255-0.09170.153633.078158.8723373.6254
120.23480.05910.07440.3972-0.31190.313-0.0772-0.09860.03330.24860.0490.2031-0.3804-0.430.09480.29660.14380.04280.5382-0.0610.391226.486673.8455354.2383
130.5128-0.0672-0.25740.05650.09550.52390.1402-0.15780.20140.0794-0.0551-0.0754-0.4054-0.1619-0.3801-0.1680.27350.17590.1609-0.13370.212430.060373.3239351.9003
140.26510.159-0.08561.09010.41760.29130.0183-0.0558-0.05690.10250.0343-0.4862-0.18780.04090.14060.86910.24260.25890.34680.17980.606330.258290.8605330.0501
150.1911-0.2181-0.08280.25230.10240.15460.0445-0.05170.2667-0.00310.1479-0.2192-0.32740.02370.01670.44130.08750.1470.40610.07470.596329.902283.5968326.1277
161.35360.5208-0.08710.2183-0.12980.37330.01370.1458-0.2979-0.0344-0.1126-0.21680.1227-0.1432-0.23040.15260.1571-0.00590.9814-0.08440.357714.350359.8611350.704
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 1:76)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 77:91)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 92:121)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 122:160)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 161:181)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 182:231)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 232:264)
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ -1:17)
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 18:33)
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 34:74)
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 75:121)
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 122:181)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 182:264)
14X-RAY DIFFRACTION14CHAIN C AND (RESSEQ 16:23)
15X-RAY DIFFRACTION15CHAIN C AND (RESSEQ 24:29)
16X-RAY DIFFRACTION16CHAIN D AND (RESSEQ 16:29)

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