[English] 日本語
Yorodumi
- PDB-7kij: Muscovy duck circovirus Rep domain complexed with a single-strand... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7kij
TitleMuscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site
Components
  • ATP-dependent helicase Rep
  • DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
KeywordsREPLICATION/DNA / HUH-tag / HUH motif / Rep domain / viral protein / single stranded DNA / ssDNA / ssDNA binding / REPLICATION / DNA BINDING PROTEIN / REPLICATION-DNA complex
Function / homology
Function and homology information


nucleotidyltransferase activity / endonuclease activity / DNA replication / RNA helicase activity / hydrolase activity / host cell nucleus / DNA binding / RNA binding / ATP binding / metal ion binding
Similarity search - Function
Putative viral replication protein / : / CRESS-DNA virus replication initiator protein (Rep) endonuclease domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / DNA / Replication-associated protein
Similarity search - Component
Biological speciesMuscovy duck circovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsTompkins, K.J. / Gordon, W.R. / Shi, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119483 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118047 United States
CitationJournal: Mbio / Year: 2023
Title: Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases.
Authors: Smiley, A.T. / Tompkins, K.J. / Pawlak, M.R. / Krueger, A.J. / Evans 3rd, R.L. / Shi, K. / Aihara, H. / Gordon, W.R.
History
DepositionOct 23, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Jun 19, 2024Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: ATP-dependent helicase Rep
D: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
A: ATP-dependent helicase Rep
B: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,29110
Polymers30,7594
Non-polymers5316
Water5,062281
1
C: ATP-dependent helicase Rep
D: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7606
Polymers15,3802
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-24 kcal/mol
Surface area6450 Å2
MethodPISA
2
A: ATP-dependent helicase Rep
B: DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5314
Polymers15,3802
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-38 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.986, 102.986, 138.294
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11B-513-

HOH

-
Components

-
Protein / DNA chain , 2 types, 4 molecules CADB

#1: Protein ATP-dependent helicase Rep / RepP / Replication-associated protein


Mass: 12385.729 Da / Num. of mol.: 2 / Mutation: Y91F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Muscovy duck circovirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2JZX8
#2: DNA chain DNA (5'-D(*TP*AP*TP*TP*AP*TP*TP*AP*CP*C)-3')


Mass: 2993.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Muscovy duck circovirus

-
Non-polymers , 4 types, 287 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.8, 2.2M ammonium sulfate, 20% glycerol added to drop

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.69→54.65 Å / Num. obs: 48935 / % possible obs: 99.84 % / Redundancy: 8.7 % / Biso Wilson estimate: 28.27 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.03628 / Rpim(I) all: 0.01275 / Rrim(I) all: 0.03856 / Net I/σ(I): 32.89
Reflection shellResolution: 1.69→1.751 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.8253 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 4791 / CC1/2: 0.784 / CC star: 0.938 / Rpim(I) all: 0.2922 / Rrim(I) all: 0.8776 / % possible all: 99.69

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WDZ

6wdz


Resolution: 1.69→54.65 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 2401 4.91 %
Rwork0.1706 46523 -
obs0.1718 48924 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.21 Å2 / Biso mean: 34.3287 Å2 / Biso min: 20.12 Å2
Refinement stepCycle: final / Resolution: 1.69→54.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1570 380 21 281 2252
Biso mean--61.27 46.66 -
Num. residues----218
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.69-1.720.40221410.334626772818100
1.72-1.760.31051550.297826492804100
1.76-1.80.26951450.254426912836100
1.8-1.850.24331330.228327012834100
1.85-1.90.22531530.206326822835100
1.9-1.950.21581170.183827132830100
1.95-2.020.22761470.165327042851100
2.02-2.090.19031260.15527122838100
2.09-2.170.18511470.151127012848100
2.17-2.270.18851240.146427412865100
2.27-2.390.1841320.156927412873100
2.39-2.540.19411260.162127352861100
2.54-2.740.20441420.172627472889100
2.74-3.010.18541530.17227652918100
3.01-3.450.19511460.166727862932100
3.45-4.340.15611580.143927992957100
4.35-54.650.19711560.18042979313599

+
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