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- PDB-5fsh: Crystal structure of Thermus thermophilus Csm6 -

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Basic information

Entry
Database: PDB / ID: 5fsh
TitleCrystal structure of Thermus thermophilus Csm6
ComponentsCSM6Six Mile Lake (South) Water Aerodrome
KeywordsHYDROLASE / CRISPR-CAS / RIBONUCLEASE / ENDONUCLEASE
Function / homologyCRISPR-associated protein (Cas_Cas02710) / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / NICKEL (II) ION / CRISPR system endoribonuclease Csm6
Function and homology information
Biological speciesTHERMUS THERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.301 Å
AuthorsNiewoehner, O. / Jinek, M.
CitationJournal: RNA / Year: 2016
Title: Structural Basis for the Endoribonuclease Activity of the Type III-A Crispr-Associated Protein Csm6.
Authors: Niewoehner, O. / Jinek, M.
History
DepositionJan 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: CSM6
B: CSM6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,2718
Polymers102,9182
Non-polymers3526
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-90.4 kcal/mol
Surface area40800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.309, 207.070, 58.903
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein CSM6 / Six Mile Lake (South) Water Aerodrome


Mass: 51459.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMUS THERMOPHILUS (bacteria) / Strain: HB8 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): ROSETTA 2 / References: UniProt: Q53W17
#2: Chemical
ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SNA SEQUENCE AT THE N-TERMINUS IS DERIVED FROM THE EXPRESSION VECTOR

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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: 2.84 Å3/Da / Density % sol: 56.6 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M HEPES PH 7.5, 14% (W/V) PEG 3400, 35 MM NICL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.3→48.7 Å / Num. obs: 98111 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.44 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 1.5 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
SLSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.301→48.701 Å / SU ML: 0.32 / σ(F): 1.35 / Phase error: 27.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 4920 5 %
Rwork0.2189 --
obs0.2202 98030 98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.1 Å2
Refinement stepCycle: LAST / Resolution: 2.301→48.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 6 72 7060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067139
X-RAY DIFFRACTIONf_angle_d0.7849655
X-RAY DIFFRACTIONf_dihedral_angle_d16.5694307
X-RAY DIFFRACTIONf_chiral_restr0.0431087
X-RAY DIFFRACTIONf_plane_restr0.0051251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3007-2.32680.3236740.37071398X-RAY DIFFRACTION43
2.3268-2.35420.33871640.32493152X-RAY DIFFRACTION99
2.3542-2.38290.33041680.30123141X-RAY DIFFRACTION100
2.3829-2.41310.27751590.29153081X-RAY DIFFRACTION100
2.4131-2.44480.32571780.27973298X-RAY DIFFRACTION100
2.4448-2.47830.32681620.28253108X-RAY DIFFRACTION100
2.4783-2.51370.30971680.27383125X-RAY DIFFRACTION100
2.5137-2.55130.32181690.27653175X-RAY DIFFRACTION100
2.5513-2.59110.32961680.28373168X-RAY DIFFRACTION100
2.5911-2.63360.33471640.28993122X-RAY DIFFRACTION100
2.6336-2.6790.32361720.2683274X-RAY DIFFRACTION100
2.679-2.72770.36171640.25813100X-RAY DIFFRACTION100
2.7277-2.78020.3311650.26723149X-RAY DIFFRACTION100
2.7802-2.83690.30211650.26353183X-RAY DIFFRACTION100
2.8369-2.89860.30651670.25853150X-RAY DIFFRACTION100
2.8986-2.9660.31111690.25123188X-RAY DIFFRACTION100
2.966-3.04020.27531660.25643146X-RAY DIFFRACTION100
3.0402-3.12240.29691650.25593181X-RAY DIFFRACTION100
3.1224-3.21420.24611660.24793173X-RAY DIFFRACTION100
3.2142-3.3180.24311670.23443159X-RAY DIFFRACTION100
3.318-3.43650.23641670.22993170X-RAY DIFFRACTION100
3.4365-3.57410.26951660.22963136X-RAY DIFFRACTION100
3.5741-3.73670.23151670.22353199X-RAY DIFFRACTION100
3.7367-3.93360.2791640.20263171X-RAY DIFFRACTION100
3.9336-4.17990.20591690.20143175X-RAY DIFFRACTION100
4.1799-4.50250.22721680.17253156X-RAY DIFFRACTION100
4.5025-4.95520.21811680.17043153X-RAY DIFFRACTION100
4.9552-5.67120.24141660.20733152X-RAY DIFFRACTION100
5.6712-7.14160.1961730.21113168X-RAY DIFFRACTION100
7.1416-48.71160.1721720.17823159X-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)
11.4523-0.1906-1.10640.50070.37013.65620.0371-0.19220.07210.2286-0.0414-0.1569-0.0486-0.1836-0.00150.57340.01440.02090.4858-0.03170.495910.206330.522448.4957
21.67471.05-0.85222.4965-0.33262.5523-0.31260.1673-0.3845-0.20520.1764-0.00730.28240.04420.02440.43310.03480.05290.4584-0.02750.565641.411611.90686.8531
30.5385-0.08990.79920.2750.08291.9497-0.26040.44151.6593-1.0947-0.4964-0.1445-0.20220.5582-3.45861.4022-0.4460.41991.1367-0.63190.07449.388921.7637-19.2691
40.5574-0.0763-0.8160.27610.73870.8045-0.28740.31990.0373-0.78390.40430.73520.237-0.36470.02240.858-0.1672-0.17740.78490.05050.651738.147320.074-4.7181
51.33810.1939-0.35031.85330.69912.2030.7808-0.25910.6659-0.4299-0.32750.7925-1.3484-0.75890.30220.51430.04720.03471.2071-0.06630.7601-18.226719.409834.4295
61.95220.65570.20942.987-0.52281.58260.0739-0.115-0.08510.0094-0.07820.22240.1249-0.42260.0010.4279-0.03050.03260.5449-0.03280.40843.455917.0833.6764
72.32460.765-0.1141.2045-0.3262.18390.03420.24240.44320.23450.33790.1243-0.4006-0.56250.19240.55480.06350.12270.5350.16080.588632.738344.949611.0304
80.4022-0.14160.56280.82130.75361.3031-0.27950.3401-0.2017-0.57780.3206-0.9342-0.41190.36720.00170.6057-0.18080.13020.5234-0.05360.8662.509737.66933.5338
90.9621-0.53880.60631.5969-0.99181.7670.0750.35710.11330.0065-0.2432-0.96930.17811.33040.01030.6747-0.062-0.02390.8247-0.09831.285568.511536.38435.9039
100.7209-0.2867-0.63383.59690.5911.4156-0.1837-0.30730.12851.03890.2177-0.7815-0.15960.29360.29030.6183-0.0052-0.07630.46390.00580.516852.474635.342413.6586
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID -2 THROUGH 207 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 208 THROUGH 366 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 367 THROUGH 401 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 402 THROUGH 464 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 0 THROUGH 51 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 52 THROUGH 207 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 208 THROUGH 319 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 320 THROUGH 366 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 367 THROUGH 401 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 402 THROUGH 464 )

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