[English] 日本語
Yorodumi
- PDB-4j0o: Structure of the Y246A Mutant of the PANTON-VALENTINE LEUCOCIDIN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j0o
TitleStructure of the Y246A Mutant of the PANTON-VALENTINE LEUCOCIDIN S Component from STAPHYLOCOCCUS AUREUS
ComponentsLukS-PV
KeywordsTOXIN / BI-COMPONENT LEUCOTOXIN / STAPHYLOCOCCUS AUREUS / S COMPONENT LEUCOCIDIN / beta-barrel pore forming toxin
Function / homology
Function and homology information


cytolysis in another organism / extracellular region
Similarity search - Function
Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus phage PVL (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMaveyraud, L. / Laventie, B.J. / Prevost, G. / Mourey, L.
Citation
Journal: Plos One / Year: 2014
Title: Residues essential for panton-valentine leukocidin s component binding to its cell receptor suggest both plasticity and adaptability in its interaction surface
Authors: Laventie, B.J. / Guerin, F. / Mourey, L. / Tawk, M.Y. / Jover, E. / Maveyraud, L. / Prevost, G.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary crystallographic data of a leucotoxin S component from Staphylococcus aureus
Authors: Guillet, V. / Keller, D. / Prevost, G. / Mourey, L.
#2: Journal: J.Biol.Chem. / Year: 2004
Title: Crystal Structure of Leucotoxin S Component NEW INSIGHT INTO THE STAPHYLOCOCCAL beta-BARREL PORE-FORMING TOXINS
Authors: Guillet, V. / Roblin, P. / Werner, S. / Coraiola, M. / Menestrina, G. / Monteil, H. / Prevost, G. / Mourey, L.
#3: Journal: Structure / Year: 1999
Title: The structure of a Staphylococcus aureus leucocidin component (LukF-PV) reveals the fold of the water-soluble species of a family of transmembrane pore-forming toxins
Authors: Pedelacq, J.D. / Maveyraud, L. / Prevost, G. / Baba-Moussa, L. / Gonzalez, A. / Courcelle, E. / Shepard, W. / Monteil, H. / Samama, J.P. / Mourey, L.
History
DepositionJan 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Apr 23, 2014Group: Database references
Revision 1.3Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LukS-PV
B: LukS-PV
C: LukS-PV
D: LukS-PV


Theoretical massNumber of molelcules
Total (without water)131,7334
Polymers131,7334
Non-polymers00
Water8,521473
1
A: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LukS-PV


Theoretical massNumber of molelcules
Total (without water)32,9331
Polymers32,9331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.110, 94.110, 306.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
LukS-PV


Mass: 32933.293 Da / Num. of mol.: 4 / Fragment: UNP residues 30-312 / Mutation: Y246A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus phage PVL (virus) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O80066
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 473 / 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: 2.58 Å3/Da / Density % sol: 52.24 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 40 % PEG 200, 0.1M NaMES, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 285K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 7, 2010
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.5→47.05 Å / Num. all: 46924 / Num. obs: 46924 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 49.67 Å2 / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.827 / Mean I/σ(I) obs: 1.9 / Num. unique all: 6622 / Rsym value: 0.827 / % possible all: 95.7

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5R

1t5r


Resolution: 2.5→46.51 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9075 / SU R Cruickshank DPI: 0.444 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: BUSTER/TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.2282 2380 5.07 %RANDOM
Rwork0.1822 ---
all0.1846 46908 --
obs0.1846 46908 96.14 %-
Displacement parametersBiso mean: 42.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.8531 Å20 Å20 Å2
2---0.8531 Å20 Å2
3---1.7063 Å2
Refine analyzeLuzzati coordinate error obs: 0.291 Å
Refinement stepCycle: LAST / Resolution: 2.5→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8761 0 0 473 9234
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.018979HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1712174HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3024SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes267HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1291HARMONIC5
X-RAY DIFFRACTIONt_it8979HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion19.04
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1161SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10015SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2768 169 5.05 %
Rwork0.2176 3175 -
all0.2206 3344 -
obs--96.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.68130.02750.38180.9450.35361.88160.0007-0.0043-0.1475-0.06820.0037-0.01590.0693-0.0381-0.0044-0.02130.019-0.0252-0.0278-0.0056-0.1502-42.811717.6273-10.4118
20.7313-0.00530.63110.9460.76894.5994-0.0153-0.1617-0.10390.14560.0602-0.01180.4506-0.1598-0.0448-0.0815-0.0182-0.0259-0.0221-0.0036-0.1945-74.8762-0.8279-35.3885
31.2183-0.65180.2031.526-0.36375.0945-0.1202-0.30740.11260.32880.20450.0498-0.62960.2993-0.0843-0.1256-0.03950.0239-0.0329-0.0076-0.2418-20.4173-0.9574-39.0121
40.93310.4237-0.79271.0664-0.83162.36910.01890.10650.1617-0.1420.0223-0.0078-0.03080.0256-0.0412-0.01170.0209-0.0024-0.04120.0353-0.1741-52.8562-19.8627-14.2942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A3 - 284
2X-RAY DIFFRACTION2{ B|* }B3 - 284
3X-RAY DIFFRACTION3{ C|* }C3 - 284
4X-RAY DIFFRACTION4{ D|* }D3 - 284

+
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