[English] 日本語
Yorodumi
- PDB-1rv5: COMPLEX OF ECORV ENDONUCLEASE WITH D(AAAGAT)/D(ATCTT) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rv5
TitleCOMPLEX OF ECORV ENDONUCLEASE WITH D(AAAGAT)/D(ATCTT)
Components
  • 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'
  • ECORV ENDONUCLEASE
KeywordsHYDROLASE/DNA / ENDONUCLEASE ECORV-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 / DNA binding / metal ion binding
Similarity search - Function
Restriction endonuclease, type II, EcoRV / Restriction endonuclease, type II, EcoRV, Proteobacteria / Restriction endonuclease EcoRV / DNA mismatch repair MutH/Restriction endonuclease, type II / DNA mismatch repair MutH/Type II restriction endonuclease superfamily / ECO RV Endonuclease; Chain A / Restriction endonuclease type II-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Type II restriction enzyme EcoRV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsHorton, N.C. / Perona, J.J.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Role of protein-induced bending in the specificity of DNA recognition: crystal structure of EcoRV endonuclease complexed with d(AAAGAT) + d(ATCTT).
Authors: Horton, N.C. / Perona, J.J.
#1: Journal: Embo J. / Year: 1993
Title: The Crystal Structure of EcoRV Endonuclease and of its Complexes with Cognate and Non-Cognate DNA Fragments
Authors: Winkler, F.K. / Banner, D.W. / Oefner, C. / Tsernoglou, D. / Brown, R.S. / Heathman, S.P. / Bryan, R.K. / Martin, P.D. / Petratos, K. / Wilson, K.S.
#2: Journal: Curr.Opin.Struct.Biol. / Year: 1992
Title: Structure and Function of Restriction Endonucleases
Authors: Winkler, F.K.
History
DepositionJun 1, 1998Deposition site: NDB / Processing site: NDB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: 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
C: 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'
D: 5'-D(*AP*AP*AP*GP*AP*T*AP*TP*CP*TP*T)-3'
A: ECORV ENDONUCLEASE
B: ECORV ENDONUCLEASE


Theoretical massNumber of molelcules
Total (without water)63,8314
Polymers63,8314
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.600, 50.400, 63.900
Angle α, β, γ (deg.)96.40, 109.20, 108.50
Int Tables number1
Cell settingtriclinic
Space group name H-MP1

-
Components

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


Mass: 3356.235 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein ECORV ENDONUCLEASE


Mass: 28559.158 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P04390, type II site-specific deoxyribonuclease
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlEcoRV11
21.0 mg/mlDNA11
35 mM11NaF
40.3 mM11AlCl3
530 mM11MgCl2
6100 mMHEPES12pH7.5
7150 mM12NaCl
810-15 %PEG400012

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 15, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 29460 / % possible obs: 80 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.078
Reflection
*PLUS
Num. measured all: 128913

-
Processing

Software
NameClassification
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: 1RVA

1rva


Resolution: 2.1→6 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000 / Data cutoff low absF: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.272 488 2 %RANDOM
Rwork0.193 ---
obs0.193 27705 80 %-
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4649 478 0 492 5619
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.62
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.483
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.272 39 1.55 %
Rwork0.304 2007 -
obs--58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PR0TOPHCSDX.PRO
X-RAY DIFFRACTION2PARNDBX.DNA0TOPNDBX.DNA
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.622
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.483

+
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