[English] 日本語
Yorodumi
- PDB-2vga: The structure of Vaccinia virus A41 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vga
TitleThe structure of Vaccinia virus A41
ComponentsPROTEIN A41
KeywordsVIRAL PROTEIN / IMMUNOMODULATOR / CHEMOKINE BINDING PROTEIN / GLYCOPROTEIN / EARLY PROTEIN
Function / homologyMajor secreted virus protein / Viral Chemokine Inhibitor; Chain A / Major secreted virus protein, 35kDa / Poxvirus chemokine inhibitor superfamily / Viral chemokine binding protein / Sandwich / extracellular region / Mainly Beta / Protein OPG170
Function and homology information
Biological speciesVACCINIA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsBahar, M.W. / Kenyon, J.C. / Putz, M.M. / Abrescia, N.G.A. / Pease, J.E. / Wise, E.L. / Stuart, D.I. / Smith, G.L. / Grimes, J.M.
CitationJournal: Plos Pathog. / Year: 2008
Title: Structure and Function of A41, a Vaccinia Virus Chemokine Binding Protein.
Authors: Bahar, M.W. / Kenyon, J.C. / Putz, M.M. / Abrescia, N.G.A. / Pease, J.E. / Wise, E.L. / Stuart, D.I. / Smith, G.L. / Grimes, J.M.
History
DepositionNov 9, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN A41


Theoretical massNumber of molelcules
Total (without water)23,7691
Polymers23,7691
Non-polymers00
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)36.608, 60.839, 50.407
Angle α, β, γ (deg.)90.00, 91.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein PROTEIN A41 / A41


Mass: 23768.859 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VACCINIA VIRUS / Strain: WESTERN RESERVE / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA(DE3)PLYS / References: UniProt: P24766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.09 % / Description: DATA COLLECTED ON BM14 FOR MAD EXPERIMENT
Crystal growDetails: 0.2 M POTASSIUM FLUORIDE, 20 % POLYETHYLENE GLYCOL 3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 17533 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 7 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXDphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.9→50.38 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 10.302 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.168 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1778 10.1 %RANDOM
Rwork0.194 ---
obs0.2 15741 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.02 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å2-1.37 Å2
2--2.88 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1551 0 0 160 1711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221585
X-RAY DIFFRACTIONr_bond_other_d0.0010.021071
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9622149
X-RAY DIFFRACTIONr_angle_other_deg1.1153.0062623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6015193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74325.40574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93515287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.51156
X-RAY DIFFRACTIONr_chiral_restr0.2030.2243
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021736
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02297
X-RAY DIFFRACTIONr_nbd_refined0.20.2265
X-RAY DIFFRACTIONr_nbd_other0.1980.21103
X-RAY DIFFRACTIONr_nbtor_refined0.180.2728
X-RAY DIFFRACTIONr_nbtor_other0.0850.2886
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2260.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2680.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.65721243
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.07831586
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6534722
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7436563
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.438 134
Rwork0.298 1168
Refinement TLS params.Method: refined / Origin x: 8.038 Å / Origin y: 17.094 Å / Origin z: 30.249 Å
111213212223313233
T-0.2075 Å2-0.0193 Å20.0741 Å2--0.1161 Å20.0461 Å2---0.3038 Å2
L2.7073 °2-0.2457 °2-0.341 °2-1.7048 °2-0.0778 °2--6.4875 °2
S-0.0299 Å °-0.0521 Å °0.114 Å °0.016 Å °-0.0554 Å °-0.0544 Å °-0.0836 Å °0.534 Å °0.0853 Å °

+
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