[English] 日本語
Yorodumi
- PDB-2ivk: Crystal structure of the periplasmic endonuclease Vvn complexed w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ivk
TitleCrystal structure of the periplasmic endonuclease Vvn complexed with a 16-bp DNA
Components
  • 5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3'
  • 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3'
  • 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3'
  • ENDONUCLEASE I
KeywordsHYDROLASE / DNASE / ENDONUCLEASE / DNA HYDROLYSIS / PROTEIN NUCLEIC ACID INTERACTIONS / DNA CLEAVAGE PREFERENCE
Function / homologyEndonuclease I / Endonuclease I / His-Me finger superfamily / endonuclease activity / metal ion binding / DNA / DNA (> 10) / Endonuclease I
Function and homology information
Biological speciesVIBRIO VULNIFICUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWang, Y.T. / Yang, W.J. / Li, C.L. / Doudeva, L.G. / Yuan, H.S.
CitationJournal: Nucleic Acids Res. / Year: 2007
Title: Structural Basis for Sequence-Dependent DNA Cleavage by Nonspecific Endonucleases.
Authors: Wang, Y.T. / Yang, W.J. / Li, C.L. / Doudeva, L.G. / Yuan, H.S.
History
DepositionJun 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENDONUCLEASE I
B: ENDONUCLEASE I
C: ENDONUCLEASE I
D: ENDONUCLEASE I
E: 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3'
F: 5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3'
G: 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3'
H: 5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3'
I: 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3'
J: 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3'


Theoretical massNumber of molelcules
Total (without water)127,15310
Polymers127,15310
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)64.636, 64.705, 79.157
Angle α, β, γ (deg.)74.45, 73.56, 75.56
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
ENDONUCLEASE I / VVN NUCLEASE


Mass: 24751.709 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO VULNIFICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / Variant (production host): DE3
References: UniProt: Q7MHK3, Hydrolases; Acting on ester bonds
#2: DNA chain 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3'


Mass: 4608.021 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3'


Mass: 4567.997 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3'


Mass: 4897.203 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 80 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 80 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, HIS 80 TO ALA ENGINEERED RESIDUE IN CHAIN B, HIS 80 TO ALA ENGINEERED RESIDUE IN CHAIN C, HIS 80 TO ALA ENGINEERED RESIDUE IN CHAIN D, HIS 80 TO ALA
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.34 %
Crystal growpH: 7
Details: 20% PEG3350, 0.2 M DI-SODIUM TARTRATE DEHYDRATE, pH 7.00

-
Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 17, 2005 / Details: MIRRORS
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→37.09 Å / Num. obs: 24597 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 83.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.3 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OUP

1oup


Resolution: 2.9→37.09 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 186489.8 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1922 7.8 %RANDOM
Rwork0.237 ---
obs0.237 24597 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 30.9015 Å2 / ksol: 0.271852 e/Å3
Displacement parametersBiso mean: 61 Å2
Baniso -1Baniso -2Baniso -3
1--5.52 Å2-14.52 Å2-10.35 Å2
2---4.06 Å2-17.18 Å2
3---9.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.53 Å
Refinement stepCycle: LAST / Resolution: 2.9→37.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6902 1868 0 111 8881
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.27
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.191.5
X-RAY DIFFRACTIONc_mcangle_it6.242
X-RAY DIFFRACTIONc_scbond_it5.672
X-RAY DIFFRACTIONc_scangle_it7.632.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 292 7.7 %
Rwork0.381 3520 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA-VVN.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
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