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- PDB-5k59: Crystal structure of LukGH from Staphylococcus aureus in complex ... -

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Basic information

Entry
Database: PDB / ID: 5k59
TitleCrystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody
Components
  • (Uncharacterized leukocidin-like protein ...) x 2
  • Fab heavy chain
  • Fab light chain
KeywordsIMMUNE SYSTEM / toxin neutralizing monoclonal antibody / conformational epitope / X-ray crystal structure
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Uncharacterized leukocidin-like protein 2 / Uncharacterized leukocidin-like protein 1 / Uncharacterized leukocidin-like protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsWelin, M. / Logan, D.T. / Badarau, A. / Mirkina, I. / Zauner, G. / Dolezilkova, I. / Nagy, E.
CitationJournal: Mabs / Year: 2016
Title: Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies.
Authors: Badarau, A. / Rouha, H. / Malafa, S. / Battles, M.B. / Walker, L. / Nielson, N. / Dolezilkova, I. / Teubenbacher, A. / Banerjee, S. / Maierhofer, B. / Weber, S. / Stulik, L. / Logan, D.T. / ...Authors: Badarau, A. / Rouha, H. / Malafa, S. / Battles, M.B. / Walker, L. / Nielson, N. / Dolezilkova, I. / Teubenbacher, A. / Banerjee, S. / Maierhofer, B. / Weber, S. / Stulik, L. / Logan, D.T. / Welin, M. / Mirkina, I. / Pleban, C. / Zauner, G. / Gross, K. / Jagerhofer, M. / Magyarics, Z. / Nagy, E.
History
DepositionMay 23, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Structure summary
Revision 1.2Oct 12, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Uncharacterized leukocidin-like protein 2
B: Uncharacterized leukocidin-like protein 1
C: Uncharacterized leukocidin-like protein 2
A: Uncharacterized leukocidin-like protein 1
H: Fab heavy chain
L: Fab light chain
E: Fab heavy chain
F: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,27211
Polymers240,9478
Non-polymers3253
Water724
1
D: Uncharacterized leukocidin-like protein 2
B: Uncharacterized leukocidin-like protein 1
E: Fab heavy chain
F: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5095
Polymers120,4744
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uncharacterized leukocidin-like protein 2
A: Uncharacterized leukocidin-like protein 1
H: Fab heavy chain
L: Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7636
Polymers120,4744
Non-polymers2892
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.790, 160.932, 119.484
Angle α, β, γ (deg.)90.00, 101.18, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12B
22A
13H
23E
14L
24F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNLYSLYSDA43 - 32238 - 317
21ASNASNLYSLYSCC43 - 32238 - 317
12GLUGLUASPASPBB11 - 30513 - 307
22GLUGLUASPASPAD11 - 30513 - 307
13GLUGLULYSLYSHE1 - 2141 - 215
23GLUGLULYSLYSEG1 - 2141 - 215
14ASPASPGLYGLYLF1 - 2121 - 212
24ASPASPGLYGLYFH1 - 2121 - 212

NCS ensembles :
ID
1
2
3
4

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Components

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Uncharacterized leukocidin-like protein ... , 2 types, 4 molecules DCBA

#1: Protein Uncharacterized leukocidin-like protein 2


Mass: 37143.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: SAUSA300_1975 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FFA2, UniProt: Q2FWP0*PLUS
#2: Protein Uncharacterized leukocidin-like protein 1


Mass: 35825.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain USA300) (bacteria)
Strain: USA300 / Gene: SAUSA300_1974 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2FFA3

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Antibody , 2 types, 4 molecules HELF

#3: Antibody Fab heavy chain


Mass: 24166.100 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO3E7 / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody Fab light chain


Mass: 23338.846 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO3E7 / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 4 types, 7 molecules

#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.2
Details: Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed ...Details: Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed solution was obtained from 40 % PEG 300, 0.1 M phosphate-citrate pH 4.2, 0.3 M NaCl, 20 mM HEPES pH 7.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2014 / Details: focusing mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→48.8 Å / Num. obs: 64655 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1
Reflection shellResolution: 2.84→2.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.4 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→48.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.912 / SU ML: 0.338 / Cross valid method: THROUGHOUT / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23727 3277 5.1 %RANDOM
Rwork0.19681 ---
obs0.19888 61207 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 73.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å22.68 Å2
2---5.01 Å20 Å2
3---1.96 Å2
Refinement stepCycle: 1 / Resolution: 2.84→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15744 0 16 4 15764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216132
X-RAY DIFFRACTIONr_bond_other_d0.0030.0214844
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.93921847
X-RAY DIFFRACTIONr_angle_other_deg0.843334335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.82951968
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00624.94751
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.678152767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0181562
X-RAY DIFFRACTIONr_chiral_restr0.0830.22367
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218269
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023749
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1974.0147914
X-RAY DIFFRACTIONr_mcbond_other2.1974.0147913
X-RAY DIFFRACTIONr_mcangle_it3.6076.0149868
X-RAY DIFFRACTIONr_mcangle_other3.6076.0159869
X-RAY DIFFRACTIONr_scbond_it2.4464.1398218
X-RAY DIFFRACTIONr_scbond_other2.4454.1398218
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.0356.11711980
X-RAY DIFFRACTIONr_long_range_B_refined5.93930.7917263
X-RAY DIFFRACTIONr_long_range_B_other5.93930.79217264
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D179770.02
12C179770.02
21B176690.04
22A176690.04
31H116210.04
32E116210.04
41L121680.02
42F121680.02
LS refinement shellResolution: 2.844→2.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 197 -
Rwork0.334 4154 -
obs--91.08 %
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)
10.80.6024-0.92174.1999-0.31382.1927-0.0673-0.2135-0.02060.4837-0.0046-0.0854-0.13780.34460.0720.29220.0242-0.06880.08290.02980.2565-33.2649-2.0157187.1258
20.63471.054-0.64013.3198-1.49151.4045-0.29370.161-0.1266-0.48710.0531-0.33350.1416-0.00180.24060.3009-0.09080.01230.0867-0.00390.2742-29.7363-0.0626161.9728
30.5791-0.46010.59154.3959-0.45261.5687-0.21190.13790.098-0.51930.249-0.19630.11230.2857-0.0370.4132-0.0786-0.01030.20020.03320.3107-47.740542.136847.101
40.7028-0.6420.75942.859-1.62471.2639-0.2233-0.11010.120.38380.0874-0.1462-0.2056-0.05620.13590.34690.128-0.03360.0717-0.01320.2301-43.739939.890472.224
50.90710.0078-0.33480.1698-0.68132.86970.0904-0.03880.18720.0924-0.1113-0.0201-0.27680.54810.02090.50050.0352-0.14620.1325-0.06920.2909-18.87856.0024114.6376
60.6410.3145-0.17960.25150.12253.55280.00850.001-0.01860.11780.04610.07380.59930.39-0.05460.54890.1847-0.11670.0786-0.03610.1849-21.8967-12.3934116.596
71.2668-0.1744-0.64511.7955-0.21981.73340.1035-0.086-0.4716-0.9852-0.3497-0.34550.26160.30670.24621.13480.09020.14840.13370.08640.354-6.528434.0274119.1957
81.0868-0.3019-0.41312.7587-0.20481.26190.11280.0382-0.047-0.9924-0.3168-0.4840.02940.19490.2040.9739-0.08240.11960.12210.09760.1639-8.295652.7495117.5686
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D43 - 323
2X-RAY DIFFRACTION2B11 - 305
3X-RAY DIFFRACTION3C42 - 323
4X-RAY DIFFRACTION4A11 - 305
5X-RAY DIFFRACTION5H1 - 218
6X-RAY DIFFRACTION6L1 - 212
7X-RAY DIFFRACTION7E1 - 215
8X-RAY DIFFRACTION8F1 - 212

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