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- PDB-3b07: Crystal structure of octameric pore form of gamma-hemolysin from ... -

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Basic information

Entry
Database: PDB / ID: 3b07
TitleCrystal structure of octameric pore form of gamma-hemolysin from Staphylococcus aureus
Components
  • Gamma-hemolysin component A
  • Gamma-hemolysin component B
KeywordsTOXIN / protein complex
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / 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
Gamma-hemolysin component B / Gamma-hemolysin component A / Gamma-hemolysin component B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.495 Å
AuthorsYamashita, K. / Kawai, Y. / Tanaka, Y. / Yao, M. / Tanaka, I.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the octameric pore of staphylococcal gamma-hemolysin reveals the beta-barrel pore formation mechanism by two components
Authors: Yamashita, K. / Kawai, Y. / Tanaka, Y. / Hirano, N. / Kaneko, J. / Tomita, N. / Ohta, M. / Kamio, Y. / Yao, M. / Tanaka, I.
History
DepositionJun 6, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Database references
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-hemolysin component B
C: Gamma-hemolysin component B
E: Gamma-hemolysin component B
G: Gamma-hemolysin component B
B: Gamma-hemolysin component A
D: Gamma-hemolysin component A
F: Gamma-hemolysin component A
H: Gamma-hemolysin component A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)274,24212
Polymers273,7708
Non-polymers4734
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34670 Å2
ΔGint-50 kcal/mol
Surface area95190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.454, 206.141, 190.299
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Gamma-hemolysin component B / protomer F / H-gamma-1 / H-gamma-I


Mass: 35256.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV2421 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q931F3, UniProt: A0A0H3JX61*PLUS
#2: Protein
Gamma-hemolysin component A / protomer S / H-gamma-2 / H-gamma-II


Mass: 33186.352 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Mu50 / Gene: SAV2419 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P0A071
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.7 Å3/Da / Density % sol: 66.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Sodium acetate, ammonium acetate, MPD, pH 4.6, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 17, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: -k,-h,-l / Fraction: 0.443
ReflectionResolution: 2.49→43.298 Å / Num. obs: 138838 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 39.415 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 14.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.49-2.650.5850.6513.4714770422483216600.70396.3
2.65-2.830.4070.4245.0915412121109209190.45699.1
2.83-3.050.2550.267.7815108519743196030.27999.3
3.05-3.340.150.1611.9114295518180180610.17199.3
3.34-3.730.0830.118.1412985516482163990.10799.5
3.73-4.310.0540.07223.5511412314585145130.07899.5
4.31-5.260.0360.05729.239657412396123550.06199.7
5.26-7.390.0410.06126.2775664973697040.06699.7
7.39-440.0270.04232.5442251568956240.04598.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIXdev_617refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1LKF, 2QK7 and 3ANZ

1lkf

2qk7

3anz


Resolution: 2.495→43.298 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / Phase error: 47.32 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 3992 2.88 %RANDOM (LATTICE SYMMETRY CONSIDERED)
Rwork0.2068 ---
obs-138828 98.91 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.436 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 129.05 Å2 / Biso mean: 43.5237 Å2 / Biso min: 5.09 Å2
Baniso -1Baniso -2Baniso -3
1--13.5408 Å2-0 Å20 Å2
2---17.2704 Å20 Å2
3---30.8111 Å2
Refinement stepCycle: LAST / Resolution: 2.495→43.298 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17896 0 32 449 18377
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918356
X-RAY DIFFRACTIONf_angle_d1.12524828
X-RAY DIFFRACTIONf_chiral_restr0.0612608
X-RAY DIFFRACTIONf_plane_restr0.0053212
X-RAY DIFFRACTIONf_dihedral_angle_d15.5436744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4963-2.53930.40251900.30136286647691
2.5393-2.58550.32551980.27916701689996
2.5855-2.63520.27512000.26486681688196
2.6352-2.6890.31681960.25436655685196
2.689-2.74740.29311970.25676717691496
2.7474-2.81130.31950.2516728692396
2.8113-2.88160.27661950.22626703689896
2.8816-2.95940.25551970.21266689688696
2.9594-3.04650.261950.21296744693996
3.0465-3.14470.26971970.22476693689097
3.1447-3.25710.23481950.22146759695497
3.2571-3.38740.26442030.21076743694696
3.3874-3.54140.25281970.19726752694997
3.5414-3.72790.20931980.19136753695197
3.7279-3.96120.18972010.18826787698897
3.9612-4.26660.19512000.18226776697697
4.2666-4.69510.19712030.17316814701797
4.6951-5.37260.19542000.18496832703297
5.3726-6.76130.24022010.22336887708897
6.7613-35.71360.21062040.18547102730697

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