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- PDB-6fjw: Streptococcus thermophilus Cas6 -

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Basic information

Entry
Database: PDB / ID: 6fjw
TitleStreptococcus thermophilus Cas6
ComponentsCas6 protein
KeywordsHYDROLASE / ribonuclease / Cas6 / CRISPR / RNA binding protein
Function / homologyCRISPR-associated protein Cas6, C-terminal / CRISPR-associated endoribonuclease Cas6 / CRISPR-associated protein, Cas6 / defense response to virus / endonuclease activity / Hydrolases; Acting on ester bonds / RNA binding / CRISPR-associated endoribonuclease Cas6
Function and homology information
Biological speciesStreptococcus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsTamulaitiene, G. / Mogila, I. / Siksnys, V. / Tamulaitis, G.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research council of LthuaniaAPP-3/2016Lithuania
CitationJournal: To be published
Title: Streptococcus thermophilus Cas6
Authors: Mogila, I. / Kazlauskiene, M. / Tamulaitiene, G. / Siksnys, V. / Tamulaitis, G.
History
DepositionJan 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _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_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cas6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7342
Polymers28,6941
Non-polymers401
Water21612
1
A: Cas6 protein
hetero molecules

A: Cas6 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4674
Polymers57,3872
Non-polymers802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area1390 Å2
ΔGint-19 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.469, 91.469, 72.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

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Components

#1: Protein Cas6 protein


Mass: 28693.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus thermophilus (bacteria) / Gene: cas6 / Plasmid: pCOLA_Duet / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A0A0A7HF73
#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


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Crystallization buffer was 0.1 M Tris-HCl (pH 8.5), 0.2 M CaCl2, 2.8% ethanol, 2.8% ethylene glycol, 2.8% 2-propanol,2.8% n-butanol, 2.8% 2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2016
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.7→79.214 Å / Num. all: 9685 / Num. obs: 9685 / % possible obs: 99.9 % / Redundancy: 20.1 % / Biso Wilson estimate: 67.05 Å2 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.024 / Rrim(I) all: 0.108 / Rsym value: 0.082 / Net I/av σ(I): 5.9 / Net I/σ(I): 29.5 / Num. measured all: 194927
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.7-2.8519.50.8790.92766114210.2090.9290.8794.199.9
2.85-3.0221.10.531.42752413070.1210.560.537.399.8
3.02-3.2320.70.2962.62573812440.0690.3170.29612.1100
3.23-3.4919.40.1594.82245211560.0390.1750.15919.7100
3.49-3.8220.80.1365.32245410780.0330.150.13626.7100
3.82-4.2720.50.07110197079590.0190.0870.07143.2100
4.27-4.9319.80.04813.8172238680.0140.0650.04859.6100
4.93-6.0420.60.04913.9151717380.0170.0790.04961.5100
6.04-8.5419.10.04115.8109825740.0190.0860.04165.8100
8.54-79.21417.70.034960153400.0160.0650.03480.7100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
SCALA3.2.19data scaling
SHELXDEphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.7→79.214 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2519 1796 9.63 %
Rwork0.2135 16848 -
obs0.2171 9666 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.66 Å2 / Biso mean: 67.1512 Å2 / Biso min: 36.16 Å2
Refinement stepCycle: final / Resolution: 2.7→79.214 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1842 0 1 12 1855
Biso mean--94.67 62.66 -
Num. residues----239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141898
X-RAY DIFFRACTIONf_angle_d0.5372577
X-RAY DIFFRACTIONf_chiral_restr0.02300
X-RAY DIFFRACTIONf_plane_restr0.002326
X-RAY DIFFRACTIONf_dihedral_angle_d10.661670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7002-2.77320.391190.30513651484
2.7732-2.85480.32081250.301612921417
2.8548-2.94690.35821450.290712821427
2.9469-3.05230.38081370.29112901427
3.0523-3.17450.27811640.266612651429
3.1745-3.3190.28791620.238512661428
3.319-3.49390.25911510.216812881439
3.4939-3.71280.30231170.226612961413
3.7128-3.99950.27051480.212112851433
3.9995-4.4020.17681390.182912921431
4.402-5.03880.16131230.152613291452
5.0388-6.3480.25461390.209512821421
6.348-79.24850.25991270.210813161443

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