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- PDB-4idj: S.Aureus a-hemolysin monomer in complex with Fab -

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Basic information

Entry
Database: PDB / ID: 4idj
TitleS.Aureus a-hemolysin monomer in complex with Fab
Components
  • Alpha-hemolysin
  • Fab Heavy chain
  • Fab Light chain
KeywordsIMMUNE SYSTEM / HEMOLYSIN complex with Fab / CYTOLYTIC PROTEIN / Fab / secreted
Function / homology
Function and homology information


cytolysis in another organism / The NLRP3 inflammasome / Purinergic signaling in leishmaniasis infection / toxin activity / extracellular region / identical protein binding
Similarity search - Function
Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Immunoglobulins ...Aerolysin/haemolysin toxin, conserved site / Aerolysin type toxins signature. / Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.36 Å
AuthorsStrop, P.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Mechanism of Action and In Vivo Efficacy of a Human-Derived Antibody against Staphylococcus aureus alpha-Hemolysin.
Authors: Foletti, D. / Strop, P. / Shaughnessy, L. / Hasa-Moreno, A. / Casas, M.G. / Russell, M. / Bee, C. / Wu, S. / Pham, A. / Zeng, Z. / Pons, J. / Rajpal, A. / Shelton, D.
History
DepositionDec 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Source and taxonomy
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3May 26, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: entity_src_gen / struct_ref_seq_dif / struct_site
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _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: Alpha-hemolysin
H: Fab Heavy chain
L: Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,2518
Polymers82,7713
Non-polymers4805
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-84 kcal/mol
Surface area31950 Å2
MethodPISA
2
A: Alpha-hemolysin
H: Fab Heavy chain
L: Fab Light chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)499,50648
Polymers496,62418
Non-polymers2,88230
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area52670 Å2
ΔGint-649 kcal/mol
Surface area174440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.188, 130.188, 308.336
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Alpha-hemolysin / Alpha-HL / Alpha-toxin


Mass: 33409.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: hla, hly / Production host: Escherichia coli (E. coli) / References: UniProt: P09616
#2: Antibody Fab Heavy chain


Mass: 25796.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293S CELLS / Organ (production host): HUMAN EMBRYONIC KIDNEY CELLS / Production host: Homo sapiens (human)
#3: Antibody Fab Light chain


Mass: 23564.824 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK 293S CELLS / Organ (production host): HUMAN EMBRYONIC KIDNEY CELLS / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4

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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: 4.56 Å3/Da / Density % sol: 73.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: 1.7M AmSO4, 4.25% isopropanol, 15% glycerol, pH 6, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2012
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 22137 / % possible obs: 96.3 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.152 / Χ2: 1.081 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.35-3.476.30.55420480.923191.3
3.47-3.616.30.35521240.737194.8
3.61-3.776.20.37921501.383196.6
3.77-3.976.30.28922181.266198.3
3.97-4.226.30.19522130.918198.2
4.22-4.556.40.14122051.112197.2
4.55-56.30.12222391.208197.1
5-5.736.20.10222441.028197.5
5.73-7.216.10.10822791.056196.6
7.21-505.70.04424171.17195.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.36 Å14.99 Å
Translation3.36 Å14.99 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
BOSdata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.36→30 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.871 / WRfactor Rfree: 0.2434 / WRfactor Rwork: 0.2102 / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.7077 / SU B: 69.828 / SU ML: 0.466 / SU R Cruickshank DPI: 0.4602 / SU Rfree: 0.5348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2964 1149 5.2 %RANDOM
Rwork0.2491 ---
obs0.2515 22084 96.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 240.76 Å2 / Biso mean: 108.4352 Å2 / Biso min: 57.03 Å2
Baniso -1Baniso -2Baniso -3
1-6.48 Å23.24 Å20 Å2
2--6.48 Å20 Å2
3----9.72 Å2
Refinement stepCycle: LAST / Resolution: 3.36→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5559 0 25 0 5584
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225730
X-RAY DIFFRACTIONr_bond_other_d0.0020.023830
X-RAY DIFFRACTIONr_angle_refined_deg1.1561.9457798
X-RAY DIFFRACTIONr_angle_other_deg0.7893.0029355
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9325718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.21124.762252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.53115945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2211526
X-RAY DIFFRACTIONr_chiral_restr0.0660.2859
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026382
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021132
X-RAY DIFFRACTIONr_nbd_refined0.2060.21213
X-RAY DIFFRACTIONr_nbd_other0.1860.24045
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22724
X-RAY DIFFRACTIONr_nbtor_other0.0840.23295
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0570.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2380.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.24
X-RAY DIFFRACTIONr_mcbond_it0.1891.54579
X-RAY DIFFRACTIONr_mcbond_other0.0241.51447
X-RAY DIFFRACTIONr_mcangle_it0.24125788
X-RAY DIFFRACTIONr_scbond_it0.39132610
X-RAY DIFFRACTIONr_scangle_it0.6064.52006
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)
17.6261-1.5912.9752.2004-1.08894.83090.0889-0.6531-0.5390.04740.2512-0.3290.48120.6871-0.3401-0.36830.1389-0.0787-0.5635-0.1313-0.3657-46.734410.355572.4449
22.86560.9516-1.27562.907-0.3196.5467-0.15830.3498-0.458-0.5890.1645-0.25850.74290.1368-0.0062-0.17220.0692-0.0104-0.496-0.2586-0.3994-50.939710.325637.1969
37.9961.76010.531310.5126-0.28632.67720.4410.45670.3183-0.6734-0.3738-0.6359-0.00920.1777-0.06720.2295-0.0496-0.01250.0064-0.4691-0.331-40.966411.93011.1755
42.29110.4532-0.28655.2012-1.10313.11930.14550.4080.0306-0.77020.2318-0.4386-0.39530.3734-0.3773-0.3917-0.02090.1071-0.2564-0.27-0.4912-45.651131.284933.3004
57.2315.91515.19069.6125.9099.7837-0.4070.35111.0769-1.1798-0.1191.9995-1.2705-0.79820.5260.69550.2576-0.05960.3819-0.13780.2666-51.528924.07150.6217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 293
2X-RAY DIFFRACTION2H1 - 114
3X-RAY DIFFRACTION3H115 - 212
4X-RAY DIFFRACTION4L1 - 107
5X-RAY DIFFRACTION5L108 - 213

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