[English] 日本語
Yorodumi
- PDB-3gwk: Structure of the homodimeric WXG-100 family protein from Streptoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gwk
TitleStructure of the homodimeric WXG-100 family protein from Streptococcus agalactiae
ComponentsPutative uncharacterized protein SAG1039
KeywordsVIRAL PROTEIN / WXG motif / Four-helical bundle
Function / homologyESAT-6-like superfamily / Type VII secretion system ESAT-6-like / Proteins of 100 residues with WXG / ESAT-6-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / ESAT-6-like protein SAG1039
Function and homology information
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsPoulsen, C. / Gries, F. / Wilmanns, M. / Song, Y.H.
CitationJournal: Plos One / Year: 2014
Title: WXG100 protein superfamily consists of three subfamilies and exhibits an alpha-helical C-terminal conserved residue pattern.
Authors: Poulsen, C. / Panjikar, S. / Holton, S.J. / Wilmanns, M. / Song, Y.H.
History
DepositionApr 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 13, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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
C: Putative uncharacterized protein SAG1039
E: Putative uncharacterized protein SAG1039
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7743
Polymers21,6782
Non-polymers961
Water8,197455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-47 kcal/mol
Surface area11290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.580, 76.580, 149.740
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11C-164-

HOH

21C-278-

HOH

31C-287-

HOH

41C-289-

HOH

51C-457-

HOH

-
Components

#1: Protein Putative uncharacterized protein SAG1039 / SAG1039


Mass: 10838.833 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Strain: 2603V/R / Gene: SAG1039 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: Q8DZR0
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.93 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl pH 8.0, 1.9M (NH4)SO4, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 2, 2008
RadiationMonochromator: Double channel-cut Si (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 64406 / Num. obs: 62862 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 18.01 Å2 / Rmerge(I) obs: 0.053
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 5.1 / Num. measured obs: 33124 / Num. unique all: 4661 / Num. unique obs: 4438 / % possible all: 95.2

-
Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GVM

3gvm


Resolution: 1.3→37.096 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.896 / SU ML: -0 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.188 1000 1.59 %1000 random reflections
Rwork0.147 ---
obs0.148 62854 97.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.704 Å2 / ksol: 0.385 e/Å3
Displacement parametersBiso max: 79.27 Å2 / Biso mean: 23.29 Å2 / Biso min: 9.75 Å2
Baniso -1Baniso -2Baniso -3
1--2.506 Å20 Å2-0 Å2
2---2.506 Å20 Å2
3----3.206 Å2
Refinement stepCycle: LAST / Resolution: 1.3→37.096 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 5 455 1980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173179
X-RAY DIFFRACTIONf_angle_d1.3185783
X-RAY DIFFRACTIONf_chiral_restr0.128262
X-RAY DIFFRACTIONf_plane_restr0.007548
X-RAY DIFFRACTIONf_dihedral_angle_d17.357841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3-1.3680.1971360.1618470860695
1.368-1.4540.2181380.1498483862196
1.454-1.5670.1731380.1298585872396
1.567-1.7240.1851410.1288722886397
1.724-1.9740.1931450.1388940908599
1.974-2.4870.1611470.12691179264100
2.487-37.1110.1981550.16595379692100

+
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