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- PDB-3roh: Crystal Structure of Leukotoxin (LukE) from Staphylococcus aureus... -

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Basic information

Entry
Database: PDB / ID: 3roh
TitleCrystal Structure of Leukotoxin (LukE) from Staphylococcus aureus subsp. aureus COL.
ComponentsLeucotoxin LukEv
KeywordsTOXIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Leukocidin-like / Leukocidin / pore-forming toxin / Membrane and cell surface proteins and peptides
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
TRIETHYLENE GLYCOL / Leucotoxin LukEv
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2016
Title: Crystal structures of the components of the Staphylococcus aureus leukotoxin ED.
Authors: Nocadello, S. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Sabini, E. / Bagnoli, F. / Grandi, G. / Anderson, W.F.
History
DepositionApr 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 2, 2016Group: Database references
Revision 1.3Mar 16, 2016Group: Source and taxonomy
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Sep 13, 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

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Assembly

Deposited unit
A: Leucotoxin LukEv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2604
Polymers37,0381
Non-polymers2213
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)133.904, 133.904, 64.473
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Leucotoxin LukEv / Variant of LukE


Mass: 37038.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Strain: NCTC 8325 / Gene: HMPREF0773_11197, lukE, lukEv, SAOUHSC_01955 / Plasmid: pET 15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q2FXB0
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 7mG/mL, 0.25M Sodium chloride, 0.01M Tris, pH 8.3. Screen: JCSG+, D7, 0.2M Lithium sulfate, 0.1M Tris, pH 8.5, 40% v/v PEG 400. VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 31, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 9573 / Num. obs: 9573 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 87.7 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 25.8
Reflection shellResolution: 3.2→3.26 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 4 / Num. unique all: 467 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T5R

1t5r


Resolution: 3.2→29.94 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.932 / SU B: 24.656 / SU ML: 0.185
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22418 459 4.8 %RANDOM
Rwork0.17845 ---
all0.18055 9098 --
obs0.18055 9098 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 107.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.2→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 12 26 2286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222311
X-RAY DIFFRACTIONr_bond_other_d0.0010.021590
X-RAY DIFFRACTIONr_angle_refined_deg1.3581.9373122
X-RAY DIFFRACTIONr_angle_other_deg0.74133874
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.5695281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.21924.732112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.27915393
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.2181510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212579
X-RAY DIFFRACTIONr_gen_planes_other00.02475
X-RAY DIFFRACTIONr_mcbond_it0.8051.51399
X-RAY DIFFRACTIONr_mcbond_other0.1221.5574
X-RAY DIFFRACTIONr_mcangle_it1.57322271
X-RAY DIFFRACTIONr_scbond_it2.1223912
X-RAY DIFFRACTIONr_scangle_it3.544.5851
LS refinement shellResolution: 3.2→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 30 -
Rwork0.294 646 -
obs-646 100 %
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)
12.97152.8993-1.92687.3872-3.37613.29250.10840.25540.21380.18280.05130.1042-0.57860.0699-0.15970.186-0.0346-0.02160.2755-0.10250.13125.955528.03212.5051
22.73583.7049-2.238210.3929-5.55584.3374-0.38290.2516-0.5909-0.54940.0731-0.64410.1760.17260.30980.2948-0.0290.05250.3128-0.20810.212529.44117.76037.5645
32.34413.2751-1.223811.5243-2.8583.2594-0.0180.14670.20850.22480.1520.3838-0.3984-0.0719-0.1340.06560.0132-0.00650.1936-0.10220.091120.731821.223816.5268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 138
2X-RAY DIFFRACTION2A139 - 215
3X-RAY DIFFRACTION3A216 - 311

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