[English] 日本語
Yorodumi
- PDB-1ev7: CRYSTAL STRUCTURE OF DNA RESTRICTION ENDONUCLEASE NAEI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ev7
TitleCRYSTAL STRUCTURE OF DNA RESTRICTION ENDONUCLEASE NAEI
ComponentsTYPE IIE RESTRICTION ENDONUCLEASE NAEI
KeywordsHYDROLASE / apo-NaeI / restriction endonuclease / topoisomerase / helix-turn-helix / CAP
Function / homology
Function and homology information


type II site-specific deoxyribonuclease / type II site-specific deoxyribonuclease activity / DNA restriction-modification system / DNA binding
Similarity search - Function
Type II restriction enzyme NaeI / Restriction endonuclease NaeI / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle ...Type II restriction enzyme NaeI / Restriction endonuclease NaeI / 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 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Type II restriction enzyme NaeI
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.38 Å
AuthorsHuai, Q. / Colandene, J.D. / Chen, Y. / Luo, F. / Zhao, Y.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of NaeI-an evolutionary bridge between DNA endonuclease and topoisomerase.
Authors: Huai, Q. / Colandene, J.D. / Chen, Y. / Luo, F. / Zhao, Y. / Topal, M.D. / Ke, H.
History
DepositionApr 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TYPE IIE RESTRICTION ENDONUCLEASE NAEI
B: TYPE IIE RESTRICTION ENDONUCLEASE NAEI


Theoretical massNumber of molelcules
Total (without water)70,7682
Polymers70,7682
Non-polymers00
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-5 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.780, 56.160, 59.050
Angle α, β, γ (deg.)90.00, 95.92, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe deposited coordinates contain a biologically active dimer of NaeI

-
Components

#1: Protein TYPE IIE RESTRICTION ENDONUCLEASE NAEI


Mass: 35384.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Plasmid: PMALC2 / Production host: Escherichia coli (E. coli)
References: UniProt: P50187, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6.1
Details: 20 mM malaic acid, 20 mM NaCl, 5 mM CaCl2, 1 mM 2-mercaptoethanol, 2% PEG3350, 1.5% ethanol, pH 6.1, MICRODIALYSIS, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMmalaic acid11
220 mM11NaCl
35 mM11CaCl2
41 mMbeta-mercaptoethanol11
52 %PEG335011
61.5 %ethanol11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.978
DetectorType: BRANDEIS - B1 / Detector: CCD / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.38→50 Å / Num. all: 68874 / Num. obs: 25755 / % possible obs: 88.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.3
Reflection shellResolution: 2.38→2.48 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.185 / Num. unique all: 2118 / % possible all: 73.7
Reflection
*PLUS
Num. measured all: 68874
Reflection shell
*PLUS
% possible obs: 73.7 %

-
Processing

Software
NameClassification
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.38→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: molecular dynamic refinement as implemented in CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.2868 2544 -Reflections were automatically selected by CNS
Rwork0.2375 ---
all-23128 --
obs-25672 79.2 %-
Refinement stepCycle: LAST / Resolution: 2.38→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4620 0 0 91 4711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3

+
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