[English] 日本語
Yorodumi
- PDB-6ek1: Crystal structure of Type IIP restriction endonuclease PfoI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ek1
TitleCrystal structure of Type IIP restriction endonuclease PfoI
Componentsrestriction endonuclease PfoI
KeywordsHYDROLASE / Restriction endonuclease / PD-(D/E)xK nuclease
Function / homologytype II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / Restriction endonuclease PfoI
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsTamulaitiene, G. / Manakova, E. / Jovaisaite, V. / Grazulis, S. / Siksnys, V.
Funding supportLithuania, 1items
OrganizationGrant numberCountry
Research Council of LithuaniaMIP-41/2013Lithuania
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family.
Authors: Tamulaitiene, G. / Manakova, E. / Jovaisaite, V. / Tamulaitis, G. / Grazulis, S. / Bochtler, M. / Siksnys, V.
History
DepositionSep 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / pdbx_database_proc
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 / _entity.formula_weight

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: restriction endonuclease PfoI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2572
Polymers35,1951
Non-polymers621
Water1086
1
A: restriction endonuclease PfoI
hetero molecules

A: restriction endonuclease PfoI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5134
Polymers70,3892
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area4210 Å2
ΔGint-15 kcal/mol
Surface area25610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.067, 48.067, 266.693
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein restriction endonuclease PfoI


Mass: 35194.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: biovar 126 / Plasmid: pBAD24 / Production host: Escherichia coli BH10B (bacteria)
References: UniProt: A0A452CST7*PLUS, type II site-specific deoxyribonuclease
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.19 Å3/Da / Density % sol: 43.84 % / Description: Bipyramidal crystals
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 6.8 mg/ml of PfoI in complex with DNA oligoduplex was mixed with reservoir solution 1:1, microseeding was used. NaHepes 0.1M, magnesium formate 0.2M, 18-20% PEG3350
PH range: 7-7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 9, 2009 / Details: OSMIC CONFOCAL MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→45.22 Å / Num. obs: 17795 / % possible obs: 98.6 % / Redundancy: 5.3 % / Biso Wilson estimate: 49.262 Å2 / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.074 / Rsym value: 0.112 / Net I/σ(I): 5.7
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1470 / Rsym value: 0.44 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.8.3_1479refinement
MOSFLM6.2.6data reduction
SCALA3.2.19data scaling
MOLREP9.2.10phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→45.219 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.2 / Phase error: 27.41
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1710 9.61 %Random selection
Rwork0.2181 ---
obs0.2233 17795 96.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.601→45.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2395 0 4 6 2405
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022457
X-RAY DIFFRACTIONf_angle_d0.5743318
X-RAY DIFFRACTIONf_dihedral_angle_d12.425898
X-RAY DIFFRACTIONf_chiral_restr0.022374
X-RAY DIFFRACTIONf_plane_restr0.002426
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6011-2.67760.4141420.29311411X-RAY DIFFRACTION99
2.6776-2.7640.31831640.28131331X-RAY DIFFRACTION99
2.764-2.86280.33531650.26571356X-RAY DIFFRACTION99
2.8628-2.97740.33951380.24521406X-RAY DIFFRACTION100
2.9774-3.11290.27211240.24341351X-RAY DIFFRACTION99
3.1129-3.27690.28741440.25121379X-RAY DIFFRACTION99
3.2769-3.48220.29851430.23921351X-RAY DIFFRACTION97
3.4822-3.75090.28851470.22671308X-RAY DIFFRACTION95
3.7509-4.12810.2421460.21331258X-RAY DIFFRACTION92
4.1281-4.72490.21291490.1721292X-RAY DIFFRACTION94
4.7249-5.95080.25041200.18881310X-RAY DIFFRACTION93
5.9508-45.22570.24881280.17691332X-RAY DIFFRACTION96

+
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