[English] 日本語
Yorodumi
- PDB-6sna: Crystal structure of Antirestriction ArdC protein from R388 plasm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sna
TitleCrystal structure of Antirestriction ArdC protein from R388 plasmid. Mn(II)-bound structure.
ComponentsArdC protein
KeywordsMETAL BINDING PROTEIN / DNA binding protein Metalloprotease Antirestriction
Function / homologyN-terminal domain of anti-restriction factor ArdC / Antirestriction, ArdC / Polyvalent protein, metallopeptidase domain / N-terminal domain of anti-restriction factor ArdC / Zincin-like metallopeptidase / single-stranded DNA binding / : / ArdC protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGonzalez-Montes, L. / Moncalian, G.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-55534-C2-2-P Spain
Spanish Ministry of Science, Innovation, and UniversitiesFPU014/0601 Spain
CitationJournal: Plos Genet. / Year: 2020
Title: ArdC, a ssDNA-binding protein with a metalloprotease domain, overpasses the recipient hsdRMS restriction system broadening conjugation host range.
Authors: Gonzalez-Montes, L. / Del Campo, I. / Garcillan-Barcia, M.P. / de la Cruz, F. / Moncalian, G.
History
DepositionAug 23, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ArdC protein
B: ArdC protein
F: ArdC protein
G: ArdC protein
J: ArdC protein
K: ArdC protein
N: ArdC protein
X: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,97116
Polymers274,5318
Non-polymers4408
Water5,927329
1
A: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
J: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
N: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
X: ArdC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3712
Polymers34,3161
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.499, 116.499, 162.123
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
ArdC protein


Mass: 34316.402 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: R388 plasmid / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ardC / Plasmid: pET29c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6I6B2
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 25 % v/v ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→54.82 Å / Num. obs: 66345 / % possible obs: 96.64 % / Redundancy: 17.5 % / Biso Wilson estimate: 47.81 Å2 / CC1/2: 0.997 / Net I/σ(I): 25.69
Reflection shellResolution: 2.7→2.85 Å / Num. unique obs: 6492 / CC1/2: 0.822

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
MOSFLM7.2.2data reduction
SCALA3.3.21data scaling
MOLREPCCP4 7.0.076phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6I89

6i89


Resolution: 2.7→54.82 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2943 --
Rwork0.2216 --
obs0.2207 63337 95.47 %
Displacement parametersBiso mean: 46.75 Å2
Refinement stepCycle: LAST / Resolution: 2.7→54.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16012 0 8 354 16374
LS refinement shellResolution: 2.7→2.74 Å
RfactorNum. reflection% reflection
Rfree0.3664 --
Rwork0.2926 2950 -
obs--97 %

+
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