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- PDB-4q7g: 1.7 Angstrom Crystal Structure of leukotoxin LukD from Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 4q7g
Title1.7 Angstrom Crystal Structure of leukotoxin LukD from Staphylococcus aureus.
ComponentsLeucotoxin LukDv
KeywordsTOXIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Leukocidin-like / Distorted Sandwich / Leukocidin
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
Leukotoxin LukD / Leucotoxin LukDv
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMinasov, G. / Nocadello, S. / Shuvalova, L. / Shatsman, S. / Kwon, K. / Bagnoli, F. / Falugi, F. / Bottomley, M. / Grandi, G. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Acta Crystallogr D Struct Biol / 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 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 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 LukDv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0832
Polymers36,8731
Non-polymers2091
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.740, 49.944, 134.868
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Leucotoxin LukDv / Variant of LukD


Mass: 36873.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: COL / Gene: hlgB, lukD, lukDv, SAS1748 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): KRXpGro7 / References: UniProt: Q6G8A9, UniProt: A0A0H2WX25*PLUS
#2: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.28 Å3/Da / Density % sol: 46.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 2.6mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCL buffer, 0.5mM TCEP; Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M BIS-TRIS, 25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, ...Details: Protein: 2.6mG/mL, 0.5M Sodium chloride, 0.01M Tris-HCL buffer, 0.5mM TCEP; Screen: Classics II (G7), 0.2M Ammonium acetate, 0.1M BIS-TRIS, 25% (w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2014 / Details: beryllium lenses
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 37802 / Num. obs: 37802 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 22.9
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 3 / Num. unique all: 1897 / Rsym value: 0.615 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1PVL

1pvl


Resolution: 1.7→27.95 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.988 / SU ML: 0.068
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19599 1876 5 %RANDOM
Rwork0.16747 ---
obs0.16891 35860 99.77 %-
all-35860 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å2-0 Å2-0 Å2
2--0.78 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 14 381 2803
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192686
X-RAY DIFFRACTIONr_bond_other_d0.0010.022425
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9253667
X-RAY DIFFRACTIONr_angle_other_deg0.67235614
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7785344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86925.612139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.95315459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.487159
X-RAY DIFFRACTIONr_chiral_restr0.0890.2376
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023250
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02671
X-RAY DIFFRACTIONr_mcbond_it1.5371.7071316
X-RAY DIFFRACTIONr_mcbond_other1.5041.7021315
X-RAY DIFFRACTIONr_mcangle_it2.4642.5581680
X-RAY DIFFRACTIONr_mcangle_other2.4712.5611681
X-RAY DIFFRACTIONr_scbond_it2.0181.911370
X-RAY DIFFRACTIONr_scbond_other2.0181.911370
X-RAY DIFFRACTIONr_scangle_other3.0872.7711988
X-RAY DIFFRACTIONr_long_range_B_refined7.20216.0383319
X-RAY DIFFRACTIONr_long_range_B_other6.90414.7493105
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 117 -
Rwork0.257 2605 -
obs-1876 99.2 %
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)
12.79-0.1645-0.5141.62610.05616.7217-0.0072-0.19030.1894-0.0439-0.01250.1192-0.1213-0.25570.01970.01790.0210.00310.04420.00350.072445.303156.79150.051
21.01010.0311.55020.22270.19392.5730.1164-0.089-0.02260.0658-0.0441-0.02320.2076-0.1631-0.07230.054-0.0263-0.00180.01650.00410.035158.844252.130514.1173
31.53830.25391.54760.5892-0.09422.9320.05340.09760.05750.0519-0.0693-0.01170.07770.15910.01590.02220.0055-0.00080.02610.00140.029563.348654.29688.4802
40.9317-0.09041.33680.12440.11872.59570.086-0.0012-0.0190.0839-0.0271-0.02040.2842-0.0078-0.05890.1056-0.0283-0.01790.02670.00970.04767.763752.040224.678
53.71150.54184.32020.58130.62565.84580.291-0.4701-0.08110.1498-0.1140.03310.5824-0.6562-0.1770.1454-0.08180.01110.10790.02450.055856.581947.946725.2256
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 47
2X-RAY DIFFRACTION2A48 - 155
3X-RAY DIFFRACTION3A156 - 183
4X-RAY DIFFRACTION4A184 - 283
5X-RAY DIFFRACTION5A284 - 325

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