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- PDB-6yes: Crystal structure of type I-D CRISPR-Cas nuclease Cas10d -

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Basic information

Entry
Database: PDB / ID: 6yes
TitleCrystal structure of type I-D CRISPR-Cas nuclease Cas10d
ComponentsCRISPR-associated protein, CscA
KeywordsDNA BINDING PROTEIN / CRISPR / Cas / archaea
Function / homologyCRISPR-associated protein, CscA
Function and homology information
Biological speciesSulfolobus islandicus LAL14/1 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.1 Å
AuthorsBrodersen, D.E. / Van, L.B. / Manav, M.C.
Funding support Denmark, 2items
OrganizationGrant numberCountry
LundbeckfondenR-287-2018-1555 Denmark
Novo Nordisk FoundationNNF17OC0028072 Denmark
CitationJournal: Nat Commun / Year: 2020
Title: Structural basis for inhibition of an archaeal CRISPR-Cas type I-D large subunit by an anti-CRISPR protein.
Authors: Manav, M.C. / Van, L.B. / Lin, J. / Fuglsang, A. / Peng, X. / Brodersen, D.E.
History
DepositionMar 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2Dec 9, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jun 30, 2021Group: Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_refine_tls / pdbx_refine_tls_group
Item: _entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene ..._entity.pdbx_description / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_asym_id / _pdbx_refine_tls_group.end_auth_asym_id / _pdbx_refine_tls_group.selection_details
Revision 1.4Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated protein, CscA
B: CRISPR-associated protein, CscA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,1074
Polymers194,9762
Non-polymers1312
Water00
1
A: CRISPR-associated protein, CscA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5532
Polymers97,4881
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CRISPR-associated protein, CscA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5532
Polymers97,4881
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)141.430, 141.430, 223.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CRISPR-associated protein, CscA


Mass: 97487.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus LAL14/1 (acidophilic)
Gene: SiL_0609 / Production host: Escherichia coli (E. coli) / References: UniProt: M9U4Y8
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
Has ligand of interestN

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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: 61 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM Hepes-NaOH 7 % (w/v) PEG8000 7 % (v/v) Ethylene glycol 1 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 4→91.31 Å / Num. obs: 23124 / % possible obs: 99.3 % / Redundancy: 9.5 % / CC1/2: 0.16 / Net I/σ(I): 0.32
Reflection shellResolution: 4.62→4.7 Å / Rmerge(I) obs: 0.52 / Num. unique obs: 674 / CC1/2: 0.4 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6THH

6thh


Resolution: 4.1→91.31 Å / SU ML: 0.79 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 44.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3703 933 4.8 %
Rwork0.3434 18510 -
obs0.3446 19443 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 612.49 Å2 / Biso mean: 263.5912 Å2 / Biso min: 136.24 Å2
Refinement stepCycle: final / Resolution: 4.1→91.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12532 0 2 0 12534
Biso mean--271.18 --
Num. residues----1567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4-4.210.41561300.45772343247389
4.21-4.470.42161550.41662598275399
4.47-4.820.44031050.392226672772100
4.82-5.30.39831290.39182667279699
5.31-6.070.41671400.40726662806100
6.07-7.650.39461430.399827092852100
7.65-91.310.32091310.27792860299198
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)
12.83523.32531.70036.9082-2.33086.1498-0.2662-0.3834-0.6959-0.03010.8088-0.49232.0977-0.3802-0.66371.61680.16710.43561.0348-0.00772.5455-51.209-33.54715.693
26.4182-1.29842.33641.0790.17451.25080.1204-0.0970.90090.2689-0.3319-0.575-1.3944-0.27970.0232.269-0.16650.26031.1760.2272.4599-10.204-9.87735.419
32.73280.4810.8321.9464-3.72048.4334-0.25890.3239-0.03420.12140.41040.23960.33640.2347-0.12431.61110.4232-0.01050.64530.0532.3512-44.208-9.088-9.528
43.8944-0.1469-0.84670.8998-1.15314.2955-0.0828-0.68740.4443-0.83670.3113-0.3096-1.4531-1.266-0.36983.6519-0.3811-0.25440.8982-0.14922.8127-60.63638.97813.999
55.4454-2.4541-1.069910.0328-5.7424.53680.7842-2.74111.80850.3925-2.6842-0.8712-0.95996.14331.80523.9358-0.3265-0.23856.034-0.23094.4891-4.71534.668-5.679
63.7053-0.87191.38061.99270.38458.96770.1385-0.44240.0835-0.78640.27970.2007-1.16710.2512-0.44611.5425-0.3125-0.27990.97580.00852.3502-45.43421.31433.173
77.8373-3.29191.33162.812-3.9097.896-0.7744-5.6841-1.24221.27442.11390.08631.3323-4.6696-0.49091.3086-0.5150.1694.8610.56883.5438-57.20212.05664.232
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 14:220 )A14 - 220
2X-RAY DIFFRACTION2( CHAIN A AND RESID 221:415 )A221 - 415
3X-RAY DIFFRACTION3( CHAIN A AND RESID 416:847 )A416 - 847
4X-RAY DIFFRACTION4( CHAIN B AND RESID 14:258 )B14 - 258
5X-RAY DIFFRACTION5( CHAIN B AND RESID 259:384 )B259 - 384
6X-RAY DIFFRACTION6( CHAIN B AND RESID 385:770 )B385 - 770
7X-RAY DIFFRACTION7( CHAIN B AND RESID 771:844 )B771 - 844

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