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- PDB-4c8z: Cas6 (TTHA0078) product complex -

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Basic information

Entry
Database: PDB / ID: 4c8z
TitleCas6 (TTHA0078) product complex
Components
  • CAS6A
  • R1 REPEAT RNA CLEAVAGE PRODUCT
KeywordsHYDROLASE/RNA / HYDROLASE-RNA COMPLEX / CRISPR CAS PROTEIN / RNA PROCESSING RIBONUCLEASE
Function / homology
Function and homology information


defense response to virus / endonuclease activity
Similarity search - Function
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) / CRISPR-associated protein Cas6 C-terminal domain-containing protein
Similarity search - Component
Biological speciesTHERMUS THERMOPHILUS HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 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 1.1Nov 20, 2013Group: Atomic model
Revision 1.2Feb 12, 2014Group: Database references
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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _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: CAS6A
B: CAS6A
C: R1 REPEAT RNA CLEAVAGE PRODUCT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5846
Polymers62,3523
Non-polymers2313
Water2,306128
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-42.9 kcal/mol
Surface area20860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.720, 83.080, 72.380
Angle α, β, γ (deg.)90.00, 100.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CAS6A


Mass: 26580.473 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 / Variant (production host): ROSETTA 2 / References: UniProt: Q5SM65
#2: RNA chain R1 REPEAT RNA CLEAVAGE PRODUCT


Mass: 9191.448 Da / Num. of mol.: 1 / Fragment: REPEAT STEM-LOOP / Source method: obtained synthetically / Details: R1 REPEAT RNA CLEAVAGE PRODUCT / Source: (synth.) THERMUS THERMOPHILUS HB8 (bacteria)
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.2 M SODIUM SULFATE, 20% (W/V) PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.999992
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999992 Å / Relative weight: 1
ReflectionResolution: 2.5→54 Å / Num. obs: 17611 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.9
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.5 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.8.2_1309)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C8Y

4c8y


Resolution: 2.503→54.034 Å / SU ML: 0.28 / σ(F): 1.99 / Phase error: 22.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2171 881 5 %
Rwork0.1765 --
obs0.1786 17611 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→54.034 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3660 300 11 128 4099
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134103
X-RAY DIFFRACTIONf_angle_d1.5335641
X-RAY DIFFRACTIONf_dihedral_angle_d15.3161562
X-RAY DIFFRACTIONf_chiral_restr0.067616
X-RAY DIFFRACTIONf_plane_restr0.007684
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.65980.26531440.2262736X-RAY DIFFRACTION99
2.6598-2.86520.25741480.21362805X-RAY DIFFRACTION100
2.8652-3.15350.26571470.20592783X-RAY DIFFRACTION100
3.1535-3.60970.21181450.18222776X-RAY DIFFRACTION100
3.6097-4.54750.2031480.14872790X-RAY DIFFRACTION100
4.5475-54.04650.17721490.15392840X-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)
12.67680.09290.41811.6985-0.43193.4564-0.0916-0.3580.34650.32660.0213-0.1253-0.4739-0.0976-0.07360.38280.068-0.06260.258-0.0450.2396-4.7351-8.81881.2319
21.6996-0.20060.82693.9045-1.66053.1416-0.0463-0.7287-0.09640.17450.73820.6232-0.3459-0.88280.20830.31750.12590.12130.4392-0.03890.3133-13.9802-11.65165.5351
32.1572-0.44381.30351.3260.04243.03240.32660.0173-0.23970.06810.01530.00250.44150.1522-0.10430.21230.0643-0.08510.1993-0.0460.2304-7.3889-22.3178-13.8678
42.27960.05341.68362.038-0.11031.32030.46250.2694-0.2591-0.6224-0.1008-0.67810.54310.3579-0.15150.46980.1418-0.06550.3276-0.04480.39361.5398-26.9262-16.6312
52.4829-0.6480.57864.0054-0.54612.96650.14620.0793-0.14660.03390.00950.18430.40480.0228-0.16250.2150.0342-0.03490.20520.01270.1353-12.9481-19.6685-19.7087
62.1531-0.99960.21082.62960.7382.42030.1412-0.143-0.32560.20750.11120.20350.52120.1171-0.15250.28570.0168-0.05780.2378-0.00590.2157-7.0084-23.7138-10.1254
71.15270.8650.13313.7017-2.01392.96960.048-0.0526-0.122-0.0065-0.0179-0.0097-0.1194-0.1642-0.04750.21890.027-0.06030.2288-0.01190.2179-30.83-25.9178-47.737
84.1332-0.7392-0.33031.63850.90724.8648-0.00680.2143-0.0379-0.4386-0.02490.1568-0.10040.306-0.1360.55440.0844-0.09590.38420.01830.2739-30.6822-23.2356-59.2085
93.32590.5520.1839.2254-5.29235.1988-0.02130.2799-0.2223-0.43860.26030.91430.1595-0.6997-0.29290.30480.0644-0.0910.3302-0.08320.3568-41.8042-27.1674-49.1035
100.88981.01780.06030.93060.2680.82460.00060.06230.11570.0637-0.0494-0.0885-0.338-0.0810.02440.29380.0764-0.05650.1516-0.02230.2706-22.2866-9.3461-45.1431
115.12481.18011.18043.7676-0.68083.77390.1123-0.7614-0.4003-0.27690.1449-0.57260.12090.2158-0.18940.2479-0.0338-0.00740.2377-0.0510.2024-14.7434-26.5454-32.9942
120.7710.2002-0.34521.9692.71246.51240.27920.0432-0.37940.05450.0077-0.19361.26470.25110.44550.23090.02740.04240.28480.01470.2544-11.1629-19.1821-43.9006
134.02930.17640.15982.6363-0.48235.04690.0193-0.0058-0.0109-0.2465-0.1054-0.6160.2450.49330.09630.2863-0.00870.03870.31440.08880.3771-3.8737-12.6341-43.7609
142.89432.13650.04965.61971.04883.51710.0544-0.0722-0.17330.77330.0611-0.01980.1734-0.27150.13540.17010.0248-0.06030.18610.00230.1384-20.8361-23.6006-28.6362
151.32920.6268-1.68743.0615-2.13123.65920.6929-0.85080.19580.6195-0.7437-0.0372-0.68630.59870.14160.179-0.0318-0.05950.35230.00550.1338-13.7343-10.9534-32.537
163.00140.9009-0.04812.1268-0.95922.2229-0.01930.19840.3111-0.1887-0.05260.3153-0.2363-0.11910.02930.25650.0715-0.02410.21960.00450.1463-18.4767-14.7006-42.5172
174.5021-0.7895-1.3435.5064-0.5082.1672-0.2512-0.1933-0.0219-0.28490.2477-0.01570.0072-0.1658-0.08620.36330.00510.02630.3540.01680.46052.3656-1.3599-22.4411
185.65421.5201-0.52831.6215-2.15313.4361-0.210.70.07480.08190.5358-1.54950.75730.8676-0.0370.26690.09350.05470.4597-0.08620.5415.795-11.5966-19.7162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 85 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 86 THROUGH 101 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 102 THROUGH 139 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 140 THROUGH 170 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 171 THROUGH 204 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 205 THROUGH 238 )
7X-RAY DIFFRACTION7CHAIN B AND (RESID 1 THROUGH 63 )
8X-RAY DIFFRACTION8CHAIN B AND (RESID 64 THROUGH 77 )
9X-RAY DIFFRACTION9CHAIN B AND (RESID 78 THROUGH 94 )
10X-RAY DIFFRACTION10CHAIN B AND (RESID 95 THROUGH 122 )
11X-RAY DIFFRACTION11CHAIN B AND (RESID 123 THROUGH 139 )
12X-RAY DIFFRACTION12CHAIN B AND (RESID 140 THROUGH 154 )
13X-RAY DIFFRACTION13CHAIN B AND (RESID 155 THROUGH 171 )
14X-RAY DIFFRACTION14CHAIN B AND (RESID 172 THROUGH 189 )
15X-RAY DIFFRACTION15CHAIN B AND (RESID 190 THROUGH 204 )
16X-RAY DIFFRACTION16CHAIN B AND (RESID 205 THROUGH 238 )
17X-RAY DIFFRACTION17CHAIN C AND (RESID 14 THROUGH 20 )
18X-RAY DIFFRACTION18CHAIN C AND (RESID 21 THROUGH 29 )

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