[English] 日本語
Yorodumi
- PDB-4ow5: Structural basis for the enhancement of virulence by entomopoxvir... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ow5
TitleStructural basis for the enhancement of virulence by entomopoxvirus fusolin and its in vivo crystallization into viral spindles
ComponentsFusolin
KeywordsVIRAL PROTEIN / Chitin-binding / LMPO / fibronectin type III fold
Function / homology: / Cellulose/chitin-binding protein, N-terminal / Lytic polysaccharide mono-oxygenase, cellulose-degrading / Immunoglobulin E-set / metal ion binding / Fusolin
Function and homology information
Biological speciesunidentified entomopoxvirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHijnen, M. / Boudes, M. / Aizel, K. / Coulibaly, F.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for the enhancement of virulence by viral spindles and their in vivo crystallization.
Authors: Chiu, E. / Hijnen, M. / Bunker, R.D. / Boudes, M. / Rajendran, C. / Aizel, K. / Olieric, V. / Schulze-Briese, C. / Mitsuhashi, W. / Young, V. / Ward, V.K. / Bergoin, M. / Metcalf, P. / Coulibaly, F.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2Apr 8, 2015Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Fusolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3298
Polymers43,8941
Non-polymers4347
Water3,549197
1
A: Fusolin
hetero molecules

A: Fusolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,65716
Polymers87,7882
Non-polymers86914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area7100 Å2
ΔGint-39 kcal/mol
Surface area28980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.270, 71.270, 129.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Fusolin


Mass: 43894.156 Da / Num. of mol.: 1 / Fragment: Chitin-binding domain / Mutation: G25D, H192N, I351N, I352H, Q353T, D354G / Source method: isolated from a natural source / Source: (natural) unidentified entomopoxvirus / References: UniProt: Q83389
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 26

-
Sample preparation

CrystalDensity Matthews: 1.88 Å3/Da / Density % sol: 34.57 %
Crystal growTemperature: 301 K / Method: in vivo crystallization / Details: crystals are obtained in vivo

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 17, 2011 / Details: Rh coated meridionally focussing mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→28.6 Å / Num. obs: 26941 / % possible obs: 98.52 % / Redundancy: 13.9 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.265 / Net I/σ(I): 10.6
Reflection shellResolution: 1.9→1.98 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.863 / Mean I/σ(I) obs: 1.9 / % possible all: 98.52

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BEM

2bem


Resolution: 1.9→28.6 Å / Cor.coef. Fo:Fc: 0.9423 / Cor.coef. Fo:Fc free: 0.9268 / SU R Cruickshank DPI: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.136 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.122
RfactorNum. reflection% reflectionSelection details
Rfree0.2025 2721 10.2 %RANDOM
Rwork0.1677 ---
obs0.1712 26671 98.52 %-
Displacement parametersBiso max: 87.46 Å2 / Biso mean: 22.64 Å2 / Biso min: 4.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.3703 Å20 Å20 Å2
2---1.3703 Å20 Å2
3---2.7405 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: final / Resolution: 1.9→28.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 70 197 2719
Biso mean--38.89 36.67 -
Num. residues----307
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1301SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes74HARMONIC2
X-RAY DIFFRACTIONt_gen_planes737HARMONIC5
X-RAY DIFFRACTIONt_it4865HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion332SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle6HARMONIC1
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5681SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d4865HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg8706HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion2.83
LS refinement shellResolution: 1.9→1.98 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2697 296 10.98 %
Rwork0.2247 2401 -
all0.2296 2697 -
obs--98.52 %

+
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