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- PDB-5yjd: Structural insights into the CRISPR-Cas-associated ribonuclease a... -

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Basic information

Entry
Database: PDB / ID: 5yjd
TitleStructural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm3
ComponentsCsm3
KeywordsHYDROLASE / CRISPR-Associated Proteins / ferredoxin-like fold / Staphylococcus epidermidis
Function / homologyCRISPR-associated RAMP Csm3 / CRISPR type III-associated protein / RAMP superfamily / defense response to virus / endonuclease activity / RNA binding / CRISPR system Cms endoribonuclease Csm3
Function and homology information
Biological speciesStaphylococcus epidermidis RP62A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsZhao, Y.Q. / Gu, Y.J. / Zhu, X.F. / Cheng, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31570842 China
CitationJournal: To Be Published
Title: Structural insights into the CRISPR-Cas-associated ribonuclease activity of Staphylococcus epidermidis Csm3 and Csm6
Authors: Zhao, Y.Q. / Gu, Y.J. / Zhu, X.F. / Cheng, W.
History
DepositionOct 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Csm3
B: Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5353
Polymers50,4952
Non-polymers401
Water1,22568
1
A: Csm3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2872
Polymers25,2471
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-8 kcal/mol
Surface area10580 Å2
MethodPISA
2
B: Csm3


Theoretical massNumber of molelcules
Total (without water)25,2471
Polymers25,2471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.623, 105.760, 155.977
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: 0 / Auth seq-ID: 3 - 216 / Label seq-ID: 3 - 216

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Csm3 / Csm3


Mass: 25247.287 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis RP62A (bacteria)
Strain: ATCC 35984 / RP62A / Gene: SERP2459 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5HK91
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.39 Å3/Da / Density % sol: 48.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 0.16M Calcium acetate, 14% (w/v) PEG8000, 20% (w/v) glycerol, 0.08M Sodium cacodylate pH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.26→52.88 Å / Num. obs: 21671 / % possible obs: 98.54 % / Redundancy: 12.2 % / Net I/σ(I): 18.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→52.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 17.767 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.209 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24097 1143 5 %RANDOM
Rwork0.19697 ---
obs0.19917 21671 98.53 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 68.99 Å2
Baniso -1Baniso -2Baniso -3
1-3.46 Å20 Å20 Å2
2--2.72 Å20 Å2
3----6.18 Å2
Refinement stepCycle: 1 / Resolution: 2.26→52.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 1 68 2994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193018
X-RAY DIFFRACTIONr_bond_other_d0.0020.022817
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9534052
X-RAY DIFFRACTIONr_angle_other_deg0.9436539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3885370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.24224.403159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92915561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9461525
X-RAY DIFFRACTIONr_chiral_restr0.0910.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023377
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02624
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_it2.882.6961489
X-RAY DIFFRACTIONr_mcbond_other2.8752.6921488
X-RAY DIFFRACTIONr_mcangle_it4.5474.0151856
X-RAY DIFFRACTIONr_mcangle_other4.5464.0211857
X-RAY DIFFRACTIONr_scbond_it4.2253.1321529
X-RAY DIFFRACTIONr_scbond_other4.2253.1351530
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6044.5342197
X-RAY DIFFRACTIONr_long_range_B_refined8.84930.9663137
X-RAY DIFFRACTIONr_long_range_B_other8.85530.9093132
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11216 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 70 -
Rwork0.373 1375 -
obs--86.94 %
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)
12.5262-0.33390.43332.5031-1.49158.64210.04420.288-0.0038-0.3113-0.09160.05440.38690.1440.04740.18240.04360.03080.16310.02180.4056-8.7347-14.9221-20.5473
25.0986-1.52441.55822.5164-1.89984.07750.27660.2971-0.0484-0.3073-0.3325-0.47160.30050.68260.05590.19320.01860.06990.27910.03610.4763.067-18.098-15.445
32.0736-0.4551.25121.8701-1.48755.33410.00410.26120.0988-0.35640.04450.0374-0.0153-0.1308-0.04860.21950.01240.01140.16180.02410.3764-11.687-12.7583-24.1331
43.1709-0.47922.06493.2237-2.00218.2504-0.07840.3050.47480.0369-0.1317-0.4213-0.63920.87540.21010.2028-0.07440.01520.20230.04120.5296-0.4964-7.7191-15.1647
56.6395-2.14961.44856.0445-2.27458.149-0.2958-0.61880.55560.60620.2295-0.2783-0.9584-0.01920.06630.31540.0590.00990.2558-0.09370.3427-8.0078-10.21860.8531
62.0357-0.3414-1.12833.0810.20237.2402-0.16420.17380.04130.69130.2622-0.2463-0.596-0.0004-0.0980.71190.0990.04790.18320.07850.4515-20.982816.0077-23.7337
71.4314-2.0975-0.96474.64431.34892.8392-0.4497-0.0783-0.05771.04440.19080.3459-0.0791-0.23850.25890.83490.07520.10820.22170.07110.3376-26.663615.1603-18.884
83.7877-1.3875-3.07843.53662.38653.0270.15970.4620.00940.0472-0.25990.2052-0.0838-0.42360.10020.4023-0.03490.05170.27640.07380.3529-21.12210.9699-39.246
94.17380.1184-0.45474.06951.70625.9685-0.4160.0364-0.38371.25840.08590.54320.219-0.51150.33010.95360.10810.26560.16780.1080.3993-29.631410.2921-15.6543
109.67253.25924.85038.32964.42546.1269-0.347-0.7638-0.76782.54380.0822-0.18381.2858-0.01270.26481.70370.25340.15060.50150.22590.4748-24.80979.4567-1.022
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 38
2X-RAY DIFFRACTION2A39 - 92
3X-RAY DIFFRACTION3A93 - 157
4X-RAY DIFFRACTION4A158 - 197
5X-RAY DIFFRACTION5A198 - 214
6X-RAY DIFFRACTION6B3 - 42
7X-RAY DIFFRACTION7B43 - 114
8X-RAY DIFFRACTION8B115 - 147
9X-RAY DIFFRACTION9B148 - 200
10X-RAY DIFFRACTION10B201 - 214

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