[English] 日本語
Yorodumi
- PDB-2ewf: Crystal structure of the site-specific DNA nickase N.BspD6I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ewf
TitleCrystal structure of the site-specific DNA nickase N.BspD6I
ComponentsNicking endonuclease N.BspD6I
KeywordsHYDROLASE / helix-turn-helix / beta-alpha-barrel
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #310 / Restriction Endonuclease - #50 / Restriction endonuclease, type II, AlwI / AlwI restriction endonuclease / Restriction Endonuclease / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Heterodimeric restriction endonuclease R.BspD6I large subunit / Nicking endonuclease N.BspD6I
Similarity search - Component
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.84 Å
AuthorsKachalova, G.S. / Bartunik, H.D. / Artyukh, R.I. / Rogulin, E.A. / Perevyazova, T.A. / Zheleznaya, L.A. / Matvienko, N.I.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Structural analysis of the heterodimeric type IIS restriction endonuclease R.BspD6I acting as a complex between a monomeric site-specific nickase and a catalytic subunit.
Authors: Kachalova, G.S. / Rogulin, E.A. / Yunusova, A.K. / Artyukh, R.I. / Perevyazova, T.A. / Matvienko, N.I. / Zheleznaya, L.A. / Bartunik, H.D.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Crystallization and preliminary crystallographic analysis of the site-specific DNA nickase Nb.BspD6I
Authors: Kachalova, G.S. / Rogulin, E.A. / Artyukh, R.I. / Perevyazova, T.A. / Zheleznaya, L.A. / Matvienko, N.I. / Bartunik, H.D.
#2: Journal: Biochemistry Mosc. / Year: 2003
Title: Cloning and sequencing of the gene of site-specific nickase N.BspD6I
Authors: Perevyazova, T.A. / Rogulin, E.A. / Zheleznaya, L.A. / Matvienko, N.I.
History
DepositionNov 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nicking endonuclease N.BspD6I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,74114
Polymers71,7021
Non-polymers1,03913
Water11,295627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.553, 92.562, 76.349
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Nicking endonuclease N.BspD6I


Mass: 71702.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: D6 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10F / References: UniProt: Q8GCA3, UniProt: A3FEV7*PLUS
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 627 / 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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 0.04 M KH2PO4, 16% (w/v) PEG 8000, 20% (v/v) glycerol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 0.9198, 0.9200, 1.05
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 25, 2005
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91981
20.921
31.051
ReflectionResolution: 1.84→20 Å / Num. obs: 67523 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.6
Reflection shellResolution: 1.84→1.87 Å / % possible all: 100

-
Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.84→10 Å / Num. parameters: 22116 / Num. restraintsaints: 20045 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.236 3330 -RANDOM
Rwork0.1829 ---
all0.2003 66117 --
obs0.2 62804 99.8 %-
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5358.79
FreeObs
Luzzati coordinate error0.1 Å0.08 Å
Luzzati d res low-8 Å
Luzzati sigma a0.23 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.84→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4861 0 13 627 5501
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.007
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.024
X-RAY DIFFRACTIONs_zero_chiral_vol0.034
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.008
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.087
X-RAY DIFFRACTIONs_approx_iso_adps0.12
LS refinement shellResolution: 1.84→1.87 Å / Redundancy reflection obs: 3131
RfactorNum. reflection% reflection
Rfree0.29 150 -
Rwork0.23 --
obs--99.8 %

+
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