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- PDB-6kc0: fused To-MtbCsm1 with 2ATP -

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Basic information

Entry
Database: PDB / ID: 6kc0
Titlefused To-MtbCsm1 with 2ATP
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 system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / HD domain profile. / GGDEF domain profile. / GGDEF domain / HD domain / HD domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
ADENOSINE-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: 2.295 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 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
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 / _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_type.id
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

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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)89,2246
Polymers88,1361
Non-polymers1,0875
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-20 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.628, 53.622, 130.313
Angle α, β, γ (deg.)90.00, 98.97, 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: 88136.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.49 %
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: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.295→64.539 Å / Num. obs: 34833 / % possible obs: 96.63 % / Redundancy: 3 % / Rpim(I) all: 0.053 / Rrim(I) all: 0.095 / Net I/σ(I): 12.31
Reflection shellResolution: 2.295→2.377 Å / Num. unique obs: 3276 / Rpim(I) all: 0.343 / Rsym value: 0.607

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Processing

Software
NameVersionClassification
PHENIX(1.14_3247: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UW2

4uw2


Resolution: 2.295→64.359 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.53
RfactorNum. reflection% reflection
Rfree0.2857 1955 5.69 %
Rwork0.2134 --
obs0.2176 34363 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.295→64.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5423 0 65 180 5668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0135616
X-RAY DIFFRACTIONf_angle_d1.3687583
X-RAY DIFFRACTIONf_dihedral_angle_d8.5073326
X-RAY DIFFRACTIONf_chiral_restr0.053808
X-RAY DIFFRACTIONf_plane_restr0.006965
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2952-2.35260.3131310.26822015X-RAY DIFFRACTION85
2.3526-2.41620.31521330.23792277X-RAY DIFFRACTION96
2.4162-2.48730.29131380.23592261X-RAY DIFFRACTION96
2.4873-2.56760.31831430.2312275X-RAY DIFFRACTION96
2.5676-2.65930.30541270.23082352X-RAY DIFFRACTION98
2.6593-2.76580.2991450.23232325X-RAY DIFFRACTION98
2.7658-2.89170.32321410.23222321X-RAY DIFFRACTION98
2.8917-3.04420.31321390.23012335X-RAY DIFFRACTION98
3.0442-3.23490.33611330.22532331X-RAY DIFFRACTION98
3.2349-3.48460.30431500.21042340X-RAY DIFFRACTION98
3.4846-3.83530.22191440.19722397X-RAY DIFFRACTION99
3.8353-4.39010.27251390.1792372X-RAY DIFFRACTION98
4.3901-5.53060.25141520.18412369X-RAY DIFFRACTION99
5.5306-64.3590.26811400.21992438X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 13.4966 Å / Origin y: 30.6729 Å / Origin z: 94.8244 Å
111213212223313233
T0.1625 Å20.0125 Å20.0215 Å2-0.075 Å20.0075 Å2--0.135 Å2
L2.2398 °2-0.2621 °20.3737 °2-0.821 °20.0097 °2--1.1709 °2
S-0.0829 Å °-0.3199 Å °-0.0332 Å °0.1822 Å °0.0579 Å °-0.0243 Å °-0.0445 Å °-0.0245 Å °-0.0129 Å °
Refinement TLS groupSelection details: all

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