[English] 日本語
Yorodumi
- PDB-1pt3: Crystal structures of nuclease-ColE7 complexed with octamer DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pt3
TitleCrystal structures of nuclease-ColE7 complexed with octamer DNA
Components
  • 5'-GCGATCGC-3'
  • Colicin E7
KeywordsHydrolase/DNA / HNH MOTIF / ENDONUCLEASE / COLICIN / PROTEIN-DNA COMPLEX / Hydrolase-DNA COMPLEX
Function / homology
Function and homology information


extrachromosomal circular DNA / endonuclease activity / killing of cells of another organism / Hydrolases; Acting on ester bonds / defense response to bacterium / metal ion binding
Similarity search - Function
Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 / Cloacin colicin family / Colicin-like bacteriocin tRNase domain / Pyosin/cloacin translocation domain / Pyosin/cloacin translocation domain superfamily / HNH nucleases / His-Me finger superfamily / HNH nuclease / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHsia, K.C. / Chak, K.F. / Cheng, Y.S. / Ku, W.Y. / Yuan, H.S.
CitationJournal: STRUCTURE / Year: 2004
Title: DNA binding and degradation by the HNH protein ColE7.
Authors: Hsia, K.C. / Chak, K.F. / Liang, P.H. / Cheng, Y.S. / Ku, W.Y. / Yuan, H.S.
History
DepositionJun 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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'-GCGATCGC-3'
D: 5'-GCGATCGC-3'
G: 5'-GCGATCGC-3'
H: 5'-GCGATCGC-3'
E: 5'-GCGATCGC-3'
F: 5'-GCGATCGC-3'
A: Colicin E7
B: Colicin E7


Theoretical massNumber of molelcules
Total (without water)43,8898
Polymers43,8898
Non-polymers00
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.430, 46.470, 78.450
Angle α, β, γ (deg.)90.00, 90.39, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S).

-
Components

#1: DNA chain
5'-GCGATCGC-3'


Mass: 2427.605 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: This sequence occurs naturally in E. coli.
#2: Protein Colicin E7 / 3.1.-.-


Mass: 14661.624 Da / Num. of mol.: 2 / Fragment: residues 449-576
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: COLE7 / Plasmid: PQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q47112, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 2.5 mM EDTA, 12.5 mM Tris-HCl (pH 7.5), 0.1 M Ammonium Formate, and 10 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.50
Components of the solutions
IDNameCrystal-IDSol-ID
1EDTA11
2Tris-HCl11
3Ammonium Formate11
4PEG 335011
5H2O11
6PEG 335012
7Ammonium Formate12
8H2O12
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22.5 mMEDTA1drop
312.5 mMTris-HCl1droppH7.5
40.1 Mammonium formate1drop
510 %PEG33501drop
60.2 Mammonium formate1reservoir
720 %PEG33501reservoir
81

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 27, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. obs: 15076 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 4.07 % / Biso Wilson estimate: 32.2 Å2 / Rsym value: 0.045 / Net I/σ(I): 36.4
Reflection shellResolution: 2.49→2.58 Å / Mean I/σ(I) obs: 7.8 / Rsym value: 0.241 / % possible all: 84.4
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 96.7 % / Num. measured all: 61443 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 83.2 % / Rmerge(I) obs: 0.236

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CEI

7cei


Resolution: 2.5→27.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 567313.87 / Data cutoff high rms absF: 567313.87 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1455 10.1 %RANDOM
Rwork0.216 ---
obs0.216 14389 95.3 %-
all-14389 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.96 Å2 / ksol: 0.29 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-5.81 Å20 Å2-0.96 Å2
2--9.19 Å20 Å2
3----15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.5 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.54 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2064 966 0 232 3262
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d4.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.262.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.399 188 8.6 %
Rwork0.301 2004 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 50 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg4.83

+
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://pdbjlvh1.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