[English] 日本語
Yorodumi
- PDB-7cfa: Crystal structure of the restriction DNA glycosylase R.CcoLI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cfa
TitleCrystal structure of the restriction DNA glycosylase R.CcoLI
ComponentsR.Pab1 family restriction endonuclease
KeywordsLYASE / glycosylase / complex
Function / homologyRestriction endonuclease, type II, Pab1 / R.Pab1 restriction endonuclease / R.Pab1 family restriction endonuclease
Function and homology information
Biological speciesCampylobacter coli (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.355 Å
AuthorsMiyazono, K. / Wang, D. / Ito, T. / Tanokura, M.
CitationJournal: Sci Rep / Year: 2021
Title: Crystal structure and DNA cleavage mechanism of the restriction DNA glycosylase R.CcoLI from Campylobacter coli.
Authors: Miyazono, K.I. / Wang, D. / Ito, T. / Tanokura, M.
History
DepositionJun 25, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.name
Revision 1.2Nov 29, 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: R.Pab1 family restriction endonuclease
B: R.Pab1 family restriction endonuclease


Theoretical massNumber of molelcules
Total (without water)56,0532
Polymers56,0532
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-24 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.493, 89.596, 100.658
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein R.Pab1 family restriction endonuclease / Restriction endonuclease


Mass: 28026.398 Da / Num. of mol.: 2 / Mutation: C189S, D225N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter coli (Campylobacter)
Gene: AXG48_08150, AXG48_09140, CJD21_04805, CJD21_09410, CYB97_01935, CYT04_03595, CYT09_05275, CYT22_08660, DNT33_05280, DZ997_05640, DZ997_09735, FDN29_08335, FPU03_05430, FRN51_06960
Plasmid: pET48b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: A0A697F4U6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0 and 8% PEG6000

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→47.17 Å / Num. obs: 25594 / % possible obs: 99.9 % / Redundancy: 7.2 % / Biso Wilson estimate: 56.271 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Net I/σ(I): 23.1 / Num. measured all: 183674 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.35-2.446.60.8651725826310.7050.3640.942.199.7
8.81-47.175.90.02333045600.9990.010.02569.198.5

-
Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHENIX1.12refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IFF

5iff


Resolution: 2.355→40.928 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.16 / Phase error: 27.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2592 2472 5.14 %
Rwork0.229 --
obs0.2306 25558 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.355→40.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3545 0 0 10 3555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023611
X-RAY DIFFRACTIONf_angle_d0.3844839
X-RAY DIFFRACTIONf_dihedral_angle_d8.5452155
X-RAY DIFFRACTIONf_chiral_restr0.041523
X-RAY DIFFRACTIONf_plane_restr0.002614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.355-2.39990.27521340.29062540X-RAY DIFFRACTION99
2.3999-2.44890.31361220.28722569X-RAY DIFFRACTION100
2.4489-2.50210.32611200.27632543X-RAY DIFFRACTION100
2.5021-2.56030.33091250.28252565X-RAY DIFFRACTION100
2.5603-2.62440.31991250.27272548X-RAY DIFFRACTION100
2.6244-2.69530.29771610.25592470X-RAY DIFFRACTION100
2.6953-2.77460.35711270.24512588X-RAY DIFFRACTION100
2.7746-2.86410.27781500.23912521X-RAY DIFFRACTION100
2.8641-2.96650.29981460.24252494X-RAY DIFFRACTION100
2.9665-3.08520.34891660.25122526X-RAY DIFFRACTION100
3.0852-3.22560.29061250.25142530X-RAY DIFFRACTION100
3.2256-3.39560.33111470.24652515X-RAY DIFFRACTION100
3.3956-3.60820.28431400.24682552X-RAY DIFFRACTION100
3.6082-3.88660.23341300.22892555X-RAY DIFFRACTION100
3.8866-4.27730.21581300.20342534X-RAY DIFFRACTION100
4.2773-4.89540.2041420.19092519X-RAY DIFFRACTION100
4.8954-6.16430.23851420.21152527X-RAY DIFFRACTION100
6.1643-40.9280.23921400.23132534X-RAY DIFFRACTION100
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)
13.5398-1.5178-0.49223.0191-0.4253.16440.1827-0.12720.3858-0.323-0.1751-0.244-0.18130.4328-0.06110.4889-0.04380.06540.3561-0.0710.470.3051-14.29191.9682
22.0223-1.6587-1.47873.43192.06151.8929-0.0055-0.23970.19080.0364-0.00290.062-0.07610.04740.15070.4017-0.0607-0.03840.4155-0.01350.4180.8016-24.45673.656
34.27580.299-0.54621.88320.35642.8245-0.12510.17480.7546-0.28020.1677-0.244-0.46260.1587-0.17770.5689-0.1486-0.03490.61010.18240.680335.0913-33.0629-22.9077
43.5179-0.063-2.4561.51140.17543.0621-0.14280.17820.3428-0.02740.1146-0.2769-0.08890.25340.06050.4176-0.0647-0.05670.44260.14810.444624.6768-37.2785-15.2525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 85 )
2X-RAY DIFFRACTION2chain 'A' and (resid 86 through 236 )
3X-RAY DIFFRACTION3chain 'B' and (resid -2 through 103 )
4X-RAY DIFFRACTION4chain 'B' and (resid 104 through 236 )

+
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