[English] 日本語
Yorodumi
- PDB-1znv: How a His-metal finger endonuclease ColE7 binds and cleaves DNA w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1znv
TitleHow a His-metal finger endonuclease ColE7 binds and cleaves DNA with a transition metal ion cofactor
Components
  • Colicin E7
  • Colicin E7 immunity protein
KeywordsHydrolase/PROTEIN BINDING / H-N-H motif / Ni-binding / protein-protein complex / endonuclease / Hydrolase-PROTEIN BINDING COMPLEX
Function / homology
Function and homology information


extrachromosomal circular DNA / bacteriocin immunity / toxic substance binding / 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 E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / Colicin/Pyocin-S2, DNase domain / Colicin/pyocin, DNase domain superfamily / Colicin, receptor domain / Coiled-coil receptor-binding R-domain of colicin E2 ...Colicin E7 immunity protein; Chain B, fragment: Endonuclease domain / Colicin/pyocin, DNase domain / Colicin E immunity protein / Colicin immunity protein/pyocin immunity protein / Colicin E immunity protein superfamily / Colicin immunity protein / pyocin immunity protein / 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 / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / Colicin-E7 immunity protein / Colicin-E7
Similarity search - Component
Biological speciesEscherichia coli str. K12 substr. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous to 1MZ8 / Resolution: 2 Å
AuthorsDoudeva, L.G. / Huang, H. / Hsia, K.C. / Shi, Z. / Li, C.L. / Shen, Y. / Yuan, H.S.
CitationJournal: Protein Sci. / Year: 2006
Title: Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn2+ or inhibitor/Ni2+
Authors: Doudeva, L.G. / Huang, H. / Hsia, K.C. / Shi, Z. / Li, C.L. / Shen, Y. / Cheng, Y.S. / Yuan, H.S.
History
DepositionMay 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Colicin E7 immunity protein
B: Colicin E7
C: Colicin E7 immunity protein
D: Colicin E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,5808
Polymers52,2734
Non-polymers3074
Water7,620423
1
A: Colicin E7 immunity protein
B: Colicin E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2904
Polymers26,1362
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Colicin E7 immunity protein
D: Colicin E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2904
Polymers26,1362
Non-polymers1542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.021, 62.882, 74.769
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Colicin E7 immunity protein / ImmE7 / Microcin E7 immunity protein


Mass: 10735.845 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: cei7 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q03708
#2: Protein Colicin E7


Mass: 15400.457 Da / Num. of mol.: 2 / Fragment: Nuclease domain / Mutation: H545E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli str. K12 substr. (bacteria)
Species: Escherichia coli / Strain: W3110 / Gene: cei7 / Plasmid: pQE70 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: Q47112, Hydrolases; Acting on ester bonds
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.3M phosphate buffer, 50mM NaCl, 20% PEG550 MME, 10% glycerol, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2004
RadiationMonochromator: double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. all: 224307 / Num. obs: 223845 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 16.3 Å2 / Rsym value: 0.082 / Net I/σ(I): 25.34
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 5.73 / Num. unique all: 4763 / Rsym value: 0.381

-
Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: Isomorphous to 1MZ8
Starting model: PDB ENTRY 1MZ8

1mz8


Resolution: 2→27.65 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 412157.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3023 8.1 %RANDOM
Rwork0.188 ---
obs0.188 37511 96.9 %-
all-38658 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.7927 Å2 / ksol: 0.374744 e/Å3
Displacement parametersBiso mean: 32.8 Å2
Baniso -1Baniso -2Baniso -3
1--9.19 Å20 Å20 Å2
2--9.56 Å20 Å2
3----0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→27.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3328 0 12 423 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.321.5
X-RAY DIFFRACTIONc_mcangle_it4.312
X-RAY DIFFRACTIONc_scbond_it5.252
X-RAY DIFFRACTIONc_scangle_it7.422.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 365 8.2 %
Rwork0.225 5373 -
obs-4338 91.1 %
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