[English] 日本語
Yorodumi
- PDB-4cgs: Crystal structure of the N-terminal domain of the PA subunit of D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cgs
TitleCrystal structure of the N-terminal domain of the PA subunit of Dhori virus polymerase
ComponentsPOLYMERASE SUBUNIT PA
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


viral RNA genome replication / RNA binding
Similarity search - Function
Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Restriction Endonuclease / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA, endonuclease domain / Influenza RNA-dependent RNA polymerase subunit PA / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polymerase subunit PA
Similarity search - Component
Biological speciesDHORI VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsGuilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S.
CitationJournal: Plos One / Year: 2014
Title: Comparative Structural and Functional Analysis of Orthomyxovirus Polymerase CAP-Snatching Domains.
Authors: Guilligay, D. / Kadlec, J. / Crepin, T. / Lunardi, T. / Bouvier, D. / Kochs, G. / Ruigrok, R.W.H. / Cusack, S.
History
DepositionNov 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POLYMERASE SUBUNIT PA
B: POLYMERASE SUBUNIT PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7204
Polymers40,5362
Non-polymers1842
Water8,503472
1
A: POLYMERASE SUBUNIT PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3602
Polymers20,2681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: POLYMERASE SUBUNIT PA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3602
Polymers20,2681
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.910, 87.450, 56.130
Angle α, β, γ (deg.)90.00, 112.98, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein POLYMERASE SUBUNIT PA


Mass: 20267.984 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DHORI VIRUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS-RIL / References: UniProt: D6PT85
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsGLYCEROL (GOL): FROM CRYOPROTECTANT

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.8 % / Description: NONE
Crystal growpH: 7.5
Details: 20MG/ML PROTEIN, 3.2 M NA FORMATE AND 0.1 M HEPES PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 92519 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 3.41 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.8
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.3 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
REFMAC5.6.0116refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.3→51.68 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.775 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21964 4640 5 %RANDOM
Rwork0.1728 ---
obs0.17509 87879 96.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.817 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.1 Å2
2--0.17 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.3→51.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2768 0 12 472 3252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192991
X-RAY DIFFRACTIONr_bond_other_d0.0050.022068
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9664072
X-RAY DIFFRACTIONr_angle_other_deg1.04135056
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.085367
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86824.333150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98615547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0651525
X-RAY DIFFRACTIONr_chiral_restr0.1210.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213344
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr5.60735059
X-RAY DIFFRACTIONr_sphericity_free24.7855121
X-RAY DIFFRACTIONr_sphericity_bonded7.20555337
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 357 -
Rwork0.23 6180 -
obs--93.59 %

+
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