[English] 日本語
Yorodumi
- PDB-5fgu: Structure of Sda1 nuclease apoprotein as an EGFP fixed-arm fusion -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fgu
TitleStructure of Sda1 nuclease apoprotein as an EGFP fixed-arm fusion
ComponentsGreen fluorescent protein,Extracellular streptodornase D
KeywordsMetal binding / DNA binding protein / beta-beta-alpha metal finger nuclease / sequence nonspecific DNA binding / Metal binding protein
Function / homology
Function and homology information


symbiont-mediated disruption of host neutrophil extracellular traps / deoxyribonuclease I activity / bioluminescence / generation of precursor metabolites and energy / nucleic acid binding / metal ion binding
Similarity search - Function
DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein ...DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Green fluorescent protein / Extracellular streptodornase D
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.896 Å
AuthorsMoon, A.F. / Krahn, J.M. / Xun, L. / Cuneo, M.J. / Pedersen, L.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ES102645 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Structural characterization of the virulence factor Sda1 nuclease from Streptococcus pyogenes.
Authors: Moon, A.F. / Krahn, J.M. / Lu, X. / Cuneo, M.J. / Pedersen, L.C.
History
DepositionDec 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein,Extracellular streptodornase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,68815
Polymers63,6281
Non-polymers1,06114
Water5,891327
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Green fluorescent protein,Extracellular streptodornase D
hetero molecules

A: Green fluorescent protein,Extracellular streptodornase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,37730
Polymers127,2552
Non-polymers2,12228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area7780 Å2
ΔGint-175 kcal/mol
Surface area41390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.407, 139.373, 120.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1504-

HOH

DetailsThe target protein was shown by SANS to be monomeric in solution.

-
Components

#1: Protein Green fluorescent protein,Extracellular streptodornase D / Phage-encoded extracellular streptodornase D / Phage-encoded streptodornase / Streptodornase


Mass: 63627.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Streptococcus pyogenes (bacteria)
Gene: GFP, sda1, sdaD2, HKU360_01468, SD90_06600 / Plasmid: pET32bEGFPX / Details (production host): EGFP fixed-arm fusion / Production host: Escherichia coli (E. coli) / References: UniProt: P42212, UniProt: Q675N6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.5 % / Description: bullet-shaped
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Crystals were grown by mixing 0.25uL of protein (13.3mg/mL) with 0.25uL mother liquor (45mM Na cacodylate pH 6, 13.5mM magnesium sulfate, 1.53M ammonium sulfate), using sitting drop vapor diffusion

-
Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.896→50 Å / Num. all: 54586 / Num. obs: 54586 / % possible obs: 100 % / Redundancy: 7.3 % / Rsym value: 0.092 / Net I/σ(I): 25.6
Reflection shellResolution: 1.896→1.93 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.54 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EGFP component of 4JRB

4jrb


Resolution: 1.896→38.276 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.93 / Stereochemistry target values: ML
Details: The authors state that the vast majority of the outliers in the structure come from regions that are not well ordered--especially residues from the C-terminal domain (residues 1336-1385). ...Details: The authors state that the vast majority of the outliers in the structure come from regions that are not well ordered--especially residues from the C-terminal domain (residues 1336-1385). This domain is largely disordered, with the exception of a few small snippets of secondary structure. These regions are not well ordered and the density is very weak, but enough to assign sequence. Occupancy refinement of these residues suggests they are present at full occupancy.
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 2733 5.01 %random selection
Rwork0.1768 ---
obs0.178 54532 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.896→38.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 62 327 4188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114041
X-RAY DIFFRACTIONf_angle_d1.2175500
X-RAY DIFFRACTIONf_dihedral_angle_d13.4841456
X-RAY DIFFRACTIONf_chiral_restr0.054598
X-RAY DIFFRACTIONf_plane_restr0.006720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8963-1.9290.25861220.22792380X-RAY DIFFRACTION92
1.929-1.96410.23451350.21432572X-RAY DIFFRACTION100
1.9641-2.00190.24681290.19852554X-RAY DIFFRACTION100
2.0019-2.04270.21361400.19422581X-RAY DIFFRACTION100
2.0427-2.08720.19861370.19242580X-RAY DIFFRACTION100
2.0872-2.13570.21731390.18232556X-RAY DIFFRACTION100
2.1357-2.18910.24421400.18972584X-RAY DIFFRACTION100
2.1891-2.24830.23691330.18862581X-RAY DIFFRACTION100
2.2483-2.31440.22741330.1922586X-RAY DIFFRACTION100
2.3144-2.38910.21941340.18482583X-RAY DIFFRACTION100
2.3891-2.47450.20911360.18922588X-RAY DIFFRACTION100
2.4745-2.57360.24461390.18762577X-RAY DIFFRACTION100
2.5736-2.69070.21011320.18992630X-RAY DIFFRACTION100
2.6907-2.83250.25481390.19342565X-RAY DIFFRACTION100
2.8325-3.00990.19611350.19662609X-RAY DIFFRACTION100
3.0099-3.24220.20971380.17442623X-RAY DIFFRACTION100
3.2422-3.56820.21881420.1652609X-RAY DIFFRACTION100
3.5682-4.0840.17641360.15342627X-RAY DIFFRACTION100
4.084-5.14350.14491440.14162660X-RAY DIFFRACTION100
5.1435-38.28420.18521500.18672754X-RAY DIFFRACTION100

+
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