[English] 日本語
Yorodumi
- PDB-2ezv: Crystal structure of tetrameric restriction endonuclease SfiI bou... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ezv
TitleCrystal structure of tetrameric restriction endonuclease SfiI bound to cognate DNA.
Components
  • 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
  • 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
  • Type II restriction enzyme SfiI
KeywordsHYDROLASE/DNA / Type IIF restriction endonuclease / protein-DNA complex / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system
Similarity search - Function
Type II restriction enzyme SfiI, DNA-recognition domain / Type II restriction enzyme SfiI, multifunctional domain / Type II restriction enzyme SfiI / Restriction endonuclease, type II SfiI, domain 2 / Restriction endonuclease, type II SfiI, domain 1 / Type II restriction enzyme SfiI / ECO RV Endonuclease; Chain A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich ...Type II restriction enzyme SfiI, DNA-recognition domain / Type II restriction enzyme SfiI, multifunctional domain / Type II restriction enzyme SfiI / Restriction endonuclease, type II SfiI, domain 2 / Restriction endonuclease, type II SfiI, domain 1 / Type II restriction enzyme SfiI / ECO RV Endonuclease; Chain A / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme SfiI
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAggarwal, A.K. / Vanamee, E.S. / Viadiu, H.
Citation
Journal: Embo J. / Year: 2005
Title: A view of consecutive binding events from structures of tetrameric endonuclease SfiI bound to DNA
Authors: Vanamee, E.S. / Viadiu, H. / Kucera, R. / Dorner, L. / Picone, S. / Schildkraut, I. / Aggarwal, A.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization of restriction endonuclease SfiI in complex with DNA.
Authors: Viadiu, H. / Vanamee, E.S. / Jacobson, E.M. / Schildkraut, I. / Aggarwal, A.K.
History
DepositionNov 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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.ptnr2_label_seq_id / _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
F: 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
G: 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
A: Type II restriction enzyme SfiI
B: Type II restriction enzyme SfiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1386
Polymers75,0574
Non-polymers802
Water3,225179
1
F: 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
G: 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
A: Type II restriction enzyme SfiI
B: Type II restriction enzyme SfiI
hetero molecules

F: 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'
G: 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'
A: Type II restriction enzyme SfiI
B: Type II restriction enzyme SfiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,27512
Polymers150,1158
Non-polymers1604
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Unit cell
Length a, b, c (Å)85.600, 85.600, 202.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: x-y,-y,1/3-z

-
Components

#1: DNA chain 5'-D(*TP*GP*GP*CP*CP*AP*AP*CP*AP*AP*GP*GP*CP*CP*T)-3'


Mass: 6447.185 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*AP*GP*GP*CP*CP*TP*TP*GP*TP*TP*GP*GP*CP*CP*A)-3'


Mass: 6438.171 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Type II restriction enzyme SfiI / Endonuclease SfiI / R.SfiI


Mass: 31086.008 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: E. coli
References: UniProt: O52512, type II site-specific deoxyribonuclease
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: pH 4.6 - 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 33075 / % possible obs: 95.9 %

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.265 1642 4.8 %
Rwork0.224 --
all-807714 -
obs-33075 95.9 %
Solvent computationBsol: 41.976 Å2
Displacement parametersBiso mean: 28.594 Å2
Baniso -1Baniso -2Baniso -3
1--1.767 Å2-3.99 Å20 Å2
2---1.767 Å20 Å2
3---3.534 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4239 609 2 179 5029
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param

+
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