[English] 日本語
Yorodumi
- PDB-6kc0: fused To-MtbCsm1 with 2ATP -

+
Open data


ID or keywords:

Loading...

-
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 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. / GGDEF domain profile. / GGDEF 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. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more