[English] 日本語
Yorodumi
- PDB-6zp9: Cyanophage S-2L Primase-Polymerase (PrimPol), AEP domain (PP-N190) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zp9
TitleCyanophage S-2L Primase-Polymerase (PrimPol), AEP domain (PP-N190)
ComponentsPrimPol AEP domain (PP-N190)
KeywordsVIRAL PROTEIN / S-2L / AEP / PrimPol / ppl1
Biological speciesCyanophage S-2L (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.50002224932 Å
AuthorsCzernecki, D. / Legrand, P. / Delarue, M.
CitationJournal: Nat Commun / Year: 2021
Title: How cyanophage S-2L rejects adenine and incorporates 2-aminoadenine to saturate hydrogen bonding in its DNA.
Authors: Czernecki, D. / Legrand, P. / Tekpinar, M. / Rosario, S. / Kaminski, P.A. / Delarue, M.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PrimPol AEP domain (PP-N190)
B: PrimPol AEP domain (PP-N190)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2065
Polymers43,0862
Non-polymers1203
Water9,890549
1
A: PrimPol AEP domain (PP-N190)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5832
Polymers21,5431
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PrimPol AEP domain (PP-N190)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6233
Polymers21,5431
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.177, 47.686, 66.155
Angle α, β, γ (deg.)90.000, 97.111, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein PrimPol AEP domain (PP-N190)


Mass: 21543.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanophage S-2L (virus) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.78 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM CaCl2; 20% w/v PEG 8k (40%); 5% v/v isopropanol (100%); 100 mM MES pH 6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980097 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 15, 2019 / Details: KB Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980097 Å / Relative weight: 1
ReflectionResolution: 1.5→47.69 Å / Num. obs: 56799 / % possible obs: 96.8 % / Redundancy: 7.1 % / Biso Wilson estimate: 16.1922278621 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.041 / Rrim(I) all: 0.11 / Net I/σ(I): 11.8
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 7 % / Rmerge(I) obs: 1.399 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4110 / CC1/2: 0.555 / Rpim(I) all: 0.563 / Rrim(I) all: 1.511 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.50002224932→41.2998111178 Å / SU ML: 0.158728224002 / Cross valid method: FREE R-VALUE / σ(F): 1.33758690843 / Phase error: 17.8886241777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172735529074 2859 5.05123674912 %
Rwork0.165656386304 53741 -
obs0.166003042424 56600 96.1832579954 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.1975881052 Å2
Refinement stepCycle: LAST / Resolution: 1.50002224932→41.2998111178 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2906 0 3 549 3458
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007430669219783041
X-RAY DIFFRACTIONf_angle_d0.8541083880984162
X-RAY DIFFRACTIONf_chiral_restr0.0564738134932452
X-RAY DIFFRACTIONf_plane_restr0.00611692011339545
X-RAY DIFFRACTIONf_dihedral_angle_d22.89526459471098
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.50002224932-1.52590.3389220844261170.2810721324342515X-RAY DIFFRACTION89.6152536602
1.5259-1.55360.2557617639411330.2498522370852574X-RAY DIFFRACTION93.056033001
1.5536-1.58350.2509698308271390.2286891172612634X-RAY DIFFRACTION94.8682860075
1.5835-1.61580.2314865649821640.2312315720282632X-RAY DIFFRACTION95.1343994556
1.6158-1.6510.2393837321731380.2177511036772667X-RAY DIFFRACTION95.2138492872
1.651-1.68940.2191789745021440.2177820327432623X-RAY DIFFRACTION95.5455801105
1.6894-1.73160.2437370130041650.2085543745012645X-RAY DIFFRACTION95.8063416297
1.7316-1.77850.2128458787771210.2030679644752665X-RAY DIFFRACTION95.7059429749
1.7785-1.83080.2188333987751430.1928386738312657X-RAY DIFFRACTION95.9890298252
1.8308-1.88990.2044098752551460.1893406226822698X-RAY DIFFRACTION96.5376782077
1.8899-1.95740.212816378841490.1752221517962685X-RAY DIFFRACTION96.5587734242
1.9574-2.03580.2070643271141350.174308494362708X-RAY DIFFRACTION96.6021066938
2.0358-2.12840.1946938181111380.1724262904812699X-RAY DIFFRACTION97.057817311
2.1284-2.24070.1625917778241370.1636313966982733X-RAY DIFFRACTION97.2551677397
2.2407-2.3810.1623089980981600.1651990183052703X-RAY DIFFRACTION97.4472430225
2.381-2.56480.1704209079731550.1654151868032713X-RAY DIFFRACTION97.7172061329
2.5648-2.82290.1661291219471440.1596696066212761X-RAY DIFFRACTION98.1750591416
2.8229-3.23120.156476818581290.1504753392742771X-RAY DIFFRACTION98.1719702099
3.2312-4.07050.109816413521510.1243818180272795X-RAY DIFFRACTION98.59437751
4.0705-41.29981111780.1490992091971510.1441325764882863X-RAY DIFFRACTION98.4967320261
Refinement TLS params.Method: refined / Origin x: 6.64609881022 Å / Origin y: 1.20881801737 Å / Origin z: 49.5152047306 Å
111213212223313233
T0.144640591065 Å2-0.00955635824357 Å20.00906316952465 Å2-0.104331338962 Å2-0.00576168601113 Å2--0.110081483348 Å2
L1.36648401825 °2-0.127500170808 °20.37226081891 °2-0.411802247484 °2-0.0947755863882 °2--0.508705419467 °2
S0.00110609951533 Å °0.0703912534987 Å °0.0102875974688 Å °-0.0487340689956 Å °-0.000896707960195 Å °0.0474493061731 Å °0.0329997608887 Å °0.00382989161612 Å °-0.000677696564672 Å °
Refinement TLS groupSelection details: all

+
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