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- PDB-3zfv: Crystal structure of an archaeal CRISPR-associated Cas6 nuclease -

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Basic information

Entry
Database: PDB / ID: 3zfv
TitleCrystal structure of an archaeal CRISPR-associated Cas6 nuclease
ComponentsCRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
KeywordsHYDROLASE
Function / homology
Function and homology information


endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds
Similarity search - Function
Cas6, N-terminal domain, archaea / Cas6 N-terminal domain / CRISPR-associated protein Cas6, C-terminal / CRISPR-associated endoribonuclease Cas6 / Alpha-Beta Plaits - #1900 / CRISPR-associated protein, Cas6 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CRISPR-associated endoribonuclease Cas6 1
Similarity search - Component
Biological speciesSULFOLOBUS SOLFATARICUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsReeks, J. / Liu, H. / White, M.F. / Naismith, J.H.
CitationJournal: Biochem.J. / Year: 2013
Title: Structure of a Dimeric Crenarchaeal Cas6 Enzyme with an Atypical Active Site for Crispr RNA Processing
Authors: Reeks, J. / Sokolowski, R. / Graham, S. / Liu, H. / Naismith, J.H. / White, M.F.
History
DepositionDec 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2013Group: Database references
Revision 1.2May 29, 2013Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
B: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
C: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
D: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,7455
Polymers132,6534
Non-polymers921
Water1629
1
A: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
B: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4193
Polymers66,3272
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-14.8 kcal/mol
Surface area24170 Å2
MethodPISA
2
C: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1

D: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1


Theoretical massNumber of molelcules
Total (without water)66,3272
Polymers66,3272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2810 Å2
ΔGint-16.5 kcal/mol
Surface area24660 Å2
MethodPISA
3
D: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1

C: CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1


Theoretical massNumber of molelcules
Total (without water)66,3272
Polymers66,3272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2810 Å2
ΔGint-16.5 kcal/mol
Surface area24660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.650, 127.460, 83.620
Angle α, β, γ (deg.)90.00, 110.48, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CRISPR-ASSOCIATED ENDORIBONUCLEASE CAS6 1 / SSO1437


Mass: 33163.285 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Production host: ESCHERICHIA COLI B (bacteria) / Strain (production host): B834
References: UniProt: Q97Y96, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FIRST SEVEN RESIDUES (GIDPFTV) ARE AN ARTIFACT OF CLONING AND REPLACE THE FIRST METHIONINE OF ...THE FIRST SEVEN RESIDUES (GIDPFTV) ARE AN ARTIFACT OF CLONING AND REPLACE THE FIRST METHIONINE OF THE NATURAL PROTEIN.

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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: 2.88 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 9.1 / Details: 0.05 M BICINE PH 9.1, 28 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→78.33 Å / Num. obs: 34686 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 10.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 23.3
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.7 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
xia2data scaling
PHENIXAUTOSOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.8→78.33 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.924 / SU B: 28.297 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R: 4.31 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED REFINEMENT WAS PERFORMED USING THE COMMAND NCSR LOCAL.
RfactorNum. reflection% reflectionSelection details
Rfree0.23557 1750 5 %RANDOM
Rwork0.20457 ---
obs0.20616 32914 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 52.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20.32 Å2
2---0.12 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 2.8→78.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8165 0 6 9 8180
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0198332
X-RAY DIFFRACTIONr_bond_other_d0.0060.025964
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.99411219
X-RAY DIFFRACTIONr_angle_other_deg1.358314539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3251015
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64122.607326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.392151551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8941565
X-RAY DIFFRACTIONr_chiral_restr0.0740.21303
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218875
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021694
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 128 -
Rwork0.324 2372 -
obs--98.89 %
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)
147.767220.4802-40.288110.3086-9.07778.8064-1.179-2.433-3.863-1.0247-0.8883-1.7859-0.89331.75652.06730.5189-0.2705-0.17850.44570.46650.83499.91281.966528.4719
28.3996-0.0606-2.66033.2369-0.82415.9089-0.1051-0.3819-0.47730.1350.1041-0.08690.8137-0.06360.0010.3830.0243-0.01060.11980.01730.167827.07741.628622.5526
33.66490.1482.04552.54320.11594.6491-0.0073-0.3724-0.35510.33850.03190.16190.4947-0.2341-0.02460.11870.00470.06510.03950.04430.12611.53716.566611.9687
44.47573.10951.50457.98132.35268.5632-0.08840.30940.4164-0.57580.26530.4033-0.4005-0.1164-0.17690.301-0.07410.09950.12020.08820.305518.516756.2441-8.1802
53.10.4379-0.22393.99631.8883.1577-0.12950.23760.1142-0.40720.00550.2456-0.4352-0.28370.1240.08070.0186-0.01690.05580.01960.10549.081332.3791-2.5104
61.82640.7988-0.973111.66048.32778.307-0.3502-0.03620.122-0.58260.42440.3251-0.11990.5607-0.07420.2168-0.0713-0.02540.15890.05520.193215.337137.9192-7.4085
78.08323.56722.28074.58432.15494.9667-0.1428-0.84790.04450.13750.1048-0.67290.16060.10880.0380.10770.1480.04870.3266-0.12620.543947.660725.341814.7297
82.86531.07360.59714.84690.83283.1046-0.0479-0.0071-0.33520.34070.2624-0.76240.24030.3901-0.21450.07520.1131-0.06060.2702-0.18230.327837.940746.891726.6255
92.74674.37271.609611.70681.9331.74320.1050.5785-0.37020.45990.4796-1.20110.30940.9764-0.58470.15070.1979-0.10750.653-0.46340.771246.400444.264921.8532
102.57010.2743-2.0114.69442.62746.6211-0.26450.06490.6492-0.5622-0.20870.5376-0.6436-0.280.47320.19590.0015-0.18310.0538-0.08380.44357.825917.0787-14.0257
113.9520.1508-0.87383.4992.36275.265-0.11620.29250.163-0.3439-0.10510.1582-0.2225-0.17580.22130.0507-0.01420.00540.0476-0.00560.315960.64713.4851-16.7204
124.35920.29810.71342.5995-0.32633.8835-0.16090.01140.2891-0.2570.17770.1438-0.272-0.1961-0.01680.0733-0.0362-0.02860.07360.05370.129447.7185-2.2656-27.1034
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 128
3X-RAY DIFFRACTION3A129 - 282
4X-RAY DIFFRACTION4B4 - 121
5X-RAY DIFFRACTION5B122 - 258
6X-RAY DIFFRACTION6B259 - 283
7X-RAY DIFFRACTION7C6 - 127
8X-RAY DIFFRACTION8C128 - 249
9X-RAY DIFFRACTION9C250 - 282
10X-RAY DIFFRACTION10D2 - 34
11X-RAY DIFFRACTION11D35 - 126
12X-RAY DIFFRACTION12D127 - 282

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