[English] 日本語
Yorodumi
- PDB-4yxa: Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yxa
TitleComplex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein
Components
  • (Surface presentation of antigens protein SpaO) x 2
  • Oxygen-regulated invasion protein OrgB,Endolysin
KeywordsPROTEIN TRANSPORT / Type III Secretion System
Function / homology
Function and homology information


bacterial-type flagellum-dependent swarming motility / protein secretion by the type III secretion system / positive chemotaxis / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / protein transport / lysozyme / lysozyme activity / host cell cytoplasm ...bacterial-type flagellum-dependent swarming motility / protein secretion by the type III secretion system / positive chemotaxis / viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / protein transport / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / cytoplasm
Similarity search - Function
Type III secretion system apparatus protein YscQ/HrcQ/SpaO / Type III secretion system outer membrane, SpaO / Surface presentation of antigens (SPOA) / SpoA-like / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme ...Type III secretion system apparatus protein YscQ/HrcQ/SpaO / Type III secretion system outer membrane, SpaO / Surface presentation of antigens (SPOA) / SpoA-like / Flagellar motor switch protein FliN-like, C-terminal domain / SpoA-like superfamily / Type III flagellar switch regulator (C-ring) FliN C-term / Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Roll / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Endolysin / SPI-1 type 3 secretion system stator protein / Surface presentation of antigens protein SpaO
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
Enterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsNotti, R.Q. / Stebbins, C.E.
CitationJournal: Nat Commun / Year: 2015
Title: A common assembly module in injectisome and flagellar type III secretion sorting platforms.
Authors: Notti, R.Q. / Bhattacharya, S. / Lilic, M. / Stebbins, C.E.
History
DepositionMar 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 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 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Surface presentation of antigens protein SpaO
B: Surface presentation of antigens protein SpaO
C: Oxygen-regulated invasion protein OrgB,Endolysin
D: Surface presentation of antigens protein SpaO
E: Surface presentation of antigens protein SpaO
F: Oxygen-regulated invasion protein OrgB,Endolysin


Theoretical massNumber of molelcules
Total (without water)76,5216
Polymers76,5216
Non-polymers00
Water2,198122
1
A: Surface presentation of antigens protein SpaO
B: Surface presentation of antigens protein SpaO
C: Oxygen-regulated invasion protein OrgB,Endolysin


Theoretical massNumber of molelcules
Total (without water)38,2613
Polymers38,2613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-38 kcal/mol
Surface area16530 Å2
MethodPISA
2
D: Surface presentation of antigens protein SpaO
E: Surface presentation of antigens protein SpaO
F: Oxygen-regulated invasion protein OrgB,Endolysin


Theoretical massNumber of molelcules
Total (without water)38,2613
Polymers38,2613
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-35 kcal/mol
Surface area16410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.880, 88.500, 63.320
Angle α, β, γ (deg.)90.000, 116.070, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Surface presentation of antigens protein SpaO


Mass: 8246.572 Da / Num. of mol.: 2 / Fragment: UNP Residues 145-213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: spaO, STM2891 / Production host: Escherichia coli (E. coli) / References: UniProt: P40699
#2: Protein Surface presentation of antigens protein SpaO


Mass: 7851.493 Da / Num. of mol.: 2 / Fragment: UNP Residues 232-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: spaO, STM2891 / Production host: Escherichia coli (E. coli) / References: UniProt: P40699
#3: Protein Oxygen-regulated invasion protein OrgB,Endolysin / Lysis protein / Lysozyme / Muramidase


Mass: 22162.568 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-30,UNP Residues 1-30 / Mutation: D20N, C54T, C97A,D20N, C54T, C97A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) (bacteria), (gene. exp.) Enterobacteria phage T4 (virus)
Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: orgB, STM2869 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CL45, UniProt: P00720, lysozyme
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium ...Details: SpaO(145-213, SeMet) + SpaO (232-297, SeMet) + OrgB(1-30)::T4 lysozyme (native) was concentrated to 18mg/mL, supplemented with 50mM maltose, and crystallized with 25% PEG3350, 200mM ammonium formate, 100mM sodium acetate pH=5.0. Microseeding was employed to enhance crystal uniformity and diffraction. Briefly, crystals to be seeded were harvested in precipitant solution and vortexed in a microfuge tube with a small stir bar for ~60 seconds. The slurry of microseeds was serially dilluted (5-10-fold steps) in precipitant solution and 5 selected microseed-precipitant mixtures were mixed with fresh protein as in a normal hanging drop experiment. Crystals were cryoprotected in 25% PEG3350, 10% ethylene glycol, 200mM ammonium formate, 100mM sodium acetate pH=5.0, 50mM maltose.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.28
ReflectionResolution: 2.35→47.61 Å / Num. obs: 25759 / % possible obs: 99 % / Redundancy: 6.6 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Net I/σ(I): 12.8 / Num. measured all: 169948 / Scaling rejects: 92
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.35-2.436.60.6172.61680925350.8160.25699.6
9.1-47.616.40.05629.525934060.9970.02386.5

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.7data scaling
PDB_EXTRACT3.15data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YX7

4yx7


Resolution: 2.35→45.804 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 35.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2618 1619 6.29 %
Rwork0.1984 24137 -
obs0.2027 25740 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.27 Å2 / Biso mean: 46.8298 Å2 / Biso min: 19.12 Å2
Refinement stepCycle: final / Resolution: 2.35→45.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 0 122 4932
Biso mean---45.62 -
Num. residues----618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114893
X-RAY DIFFRACTIONf_angle_d1.4646624
X-RAY DIFFRACTIONf_chiral_restr0.054774
X-RAY DIFFRACTIONf_plane_restr0.007843
X-RAY DIFFRACTIONf_dihedral_angle_d17.4291804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3501-2.4260.35851320.28842200233294
2.426-2.51260.30751720.28342186235892
2.5126-2.61320.38321330.29022198233194
2.6132-2.73210.3491400.2822205234593
2.7321-2.8760.32061440.26322198234293
2.876-3.05610.30841500.24732185233593
3.0561-3.29190.24591580.23122201235993
3.2919-3.62280.27081460.2052171231793
3.6228-4.14620.21271450.16572206235192
4.1462-5.22060.19291410.13572190233192
5.2206-33.40810.27881390.1652197233691

+
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