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- PDB-6kbd: fused To-MtbCsm1 with 2dATP -

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Basic information

Entry
Database: PDB / ID: 6kbd
Titlefused To-MtbCsm1 with 2dATP
ComponentsCRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A),CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
KeywordsDNA BINDING PROTEIN / Csm1 / polymersase
Function / homology
Function and homology information


exonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / endonuclease activity / defense response to virus / Hydrolases; Acting on ester bonds / RNA binding / extracellular region / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
: / CRISPR RNA silencing complex Cmr2 subunit, second helical domain / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : / Cas10/Cmr2, second palm domain / HD domain profile. / HD domain ...: / CRISPR RNA silencing complex Cmr2 subunit, second helical domain / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : / Cas10/Cmr2, second palm domain / HD domain profile. / HD domain / GGDEF domain profile. / GGDEF domain / HD domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
Similarity search - Component
Biological speciesThermococcus onnurineus NA1 (archaea)
Mycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLi, T. / Huo, Y. / Jiang, T.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Int.J.Biol.Macromol. / Year: 2020
Title: Mycobacterium tuberculosis CRISPR/Cas system Csm1 holds clues to the evolutionary relationship between DNA polymerase and cyclase activity.
Authors: Zhang, S. / Li, T. / Huo, Y. / Yang, J. / Fleming, J. / Shi, M. / Wang, Y. / Wei, W. / Gu, S. / Bi, L. / Jiang, T. / Zhang, H.
History
DepositionJun 24, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A),CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2735
Polymers89,2421
Non-polymers1,0314
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-18 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.801, 53.317, 124.134
Angle α, β, γ (deg.)90.00, 97.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A),CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / ssDNase Cas10 / Cyclic oligoadenylate synthase / ToCsm1 / ssDNase Cas10 / Cyclic oligoadenylate synthase


Mass: 89241.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 2dATP,2dATP
Source: (gene. exp.) Thermococcus onnurineus NA1 (archaea), (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: NA1, ATCC 25618 / H37Rv / Gene: csm1, cas10, TON_0893, cas10, csm1, Rv2823c / Production host: Escherichia coli (E. coli)
References: UniProt: B6YWB8, UniProt: P71629, Hydrolases; Acting on ester bonds, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestY
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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M BICINE pH 8.7 and 15% PEG 1,500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 15522 / % possible obs: 98.37 % / Redundancy: 5.9 % / CC1/2: 0.855 / Rpim(I) all: 0.092 / Rrim(I) all: 0.222 / Net I/σ(I): 23.6
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 759 / CC1/2: 0.83 / Rpim(I) all: 0.283 / Rrim(I) all: 0.636

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UW2

4uw2


Resolution: 3→41 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.2835 735 -
Rwork0.2374 --
obs-15198 99.13 %
Refinement stepCycle: LAST / Resolution: 3→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4924 0 62 0 4986
LS refinement shellResolution: 3→3.107 Å
RfactorNum. reflection% reflection
Rfree0.4075 73 -
Rwork0.2874 1505 -
obs--99.73 %

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