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- PDB-7t82: Crystal Structure of LEUKOCIDIN E/CENTYRIN S26/FAB B438 -

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Basic information

Entry
Database: PDB / ID: 7t82
TitleCrystal Structure of LEUKOCIDIN E/CENTYRIN S26/FAB B438
Components
  • Antibody Fab Heavy Chain
  • Antibody Fab Light Chain
  • Centyrin S26
  • Leukocidin E
KeywordsTOXIN / Staphylococcus aureus / SD Repeat / Phospho SD peptide / Fab / CR5133
Function / homologyLeukocidin/porin MspA / Leukocidin-like / Distorted Sandwich / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesStaphylococcaceae (Staphylococcus group)
Mus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
Model detailsCrystal Structure of Fab CR5133 / Phospho-SD Peptide Complex
AuthorsLuo, J. / Malia, T.J. / Buckley, P.T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Host Microbe / Year: 2023
Title: Multivalent human antibody-centyrin fusion protein to prevent and treat Staphylococcus aureus infections.
Authors: Buckley, P.T. / Chan, R. / Fernandez, J. / Luo, J. / Lacey, K.A. / DuMont, A.L. / O'Malley, A. / Brezski, R.J. / Zheng, S. / Malia, T. / Whitaker, B. / Zwolak, A. / Payne, A. / Clark, D. / ...Authors: Buckley, P.T. / Chan, R. / Fernandez, J. / Luo, J. / Lacey, K.A. / DuMont, A.L. / O'Malley, A. / Brezski, R.J. / Zheng, S. / Malia, T. / Whitaker, B. / Zwolak, A. / Payne, A. / Clark, D. / Sigg, M. / Lacy, E.R. / Kornilova, A. / Kwok, D. / McCarthy, S. / Wu, B. / Morrow, B. / Nemeth-Seay, J. / Petley, T. / Wu, S. / Strohl, W.R. / Lynch, A.S. / Torres, V.J.
History
DepositionDec 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 24, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Leukocidin E
B: Leukocidin E
C: Antibody Fab Light Chain
D: Antibody Fab Heavy Chain
E: Centyrin S26
F: Centyrin S26
L: Antibody Fab Light Chain
H: Antibody Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)184,7448
Polymers184,7448
Non-polymers00
Water00
1
A: Leukocidin E
C: Antibody Fab Light Chain
D: Antibody Fab Heavy Chain
F: Centyrin S26


Theoretical massNumber of molelcules
Total (without water)92,3724
Polymers92,3724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Leukocidin E
E: Centyrin S26
L: Antibody Fab Light Chain
H: Antibody Fab Heavy Chain


Theoretical massNumber of molelcules
Total (without water)92,3724
Polymers92,3724
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)344.260, 54.770, 115.730
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Leukocidin E


Mass: 33150.844 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Staphylococcaceae (Staphylococcus group)
#2: Antibody Antibody Fab Light Chain


Mass: 24005.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#3: Antibody Antibody Fab Heavy Chain


Mass: 24540.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Protein Centyrin S26


Mass: 10674.905 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
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: 2.88 Å3/Da / Density % sol: 57.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M Tri-ammonium citrate, 16 % PEG 3350, 5% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2016 / Details: mirrors
RadiationMonochromator: ACCEL SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→46.43 Å / Num. obs: 27109 / % possible obs: 99.3 % / Redundancy: 3.277 % / Biso Wilson estimate: 64.654 Å2 / CC1/2: 0.969 / Rmerge(I) obs: 0.241 / Rrim(I) all: 0.289 / Χ2: 0.797 / Net I/σ(I): 6.19 / Num. measured all: 88842 / Scaling rejects: 20
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
3.5-3.593.2191.1781.576367198319780.5091.41799.7
3.59-3.693.2180.9461.846249195219420.5391.13599.5
3.69-3.83.3590.8372.156262187318640.6260.99799.5
3.8-3.913.1980.6322.696005188718780.730.76399.5
3.91-4.043.410.5613.145878173017240.8040.66699.7
4.04-4.183.4650.3944.256063175017500.890.466100
4.18-4.343.4240.3374.975584163616310.9070.499.7
4.34-4.523.4160.2796.065500162316100.9350.33199.2
4.52-4.723.3340.2266.975165155615490.950.2799.6
4.72-4.953.2520.2217.144832149414860.9490.26599.5
4.95-5.223.0660.2117.094163137813580.9430.25798.5
5.22-5.533.1950.2017.114262135013340.9490.24298.8
5.53-5.923.1160.2096.743861125312390.9420.25398.9
5.92-6.393.3960.1997.13977117911710.9470.23799.3
6.39-73.4010.168.383680109210820.9720.1999.1
7-7.833.2850.11410.832429919870.9770.13699.6
7.83-9.043.1530.07514.4727248738640.9910.0999
9.04-11.072.9370.05118.4321947577470.9940.06298.7
11.07-15.653.0950.04719.5418015885820.9960.05799
15.65-46.433.1020.04220.0810333573330.9970.0593.3

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Processing

Software
NameVersionClassification
PHENIX1.8-3855refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3roh

3roh


Resolution: 3.5→46.43 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2789 1353 4.99 %
Rwork0.2288 25737 -
obs0.2314 27090 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.96 Å2 / Biso mean: 103.8105 Å2 / Biso min: 48.26 Å2
Refinement stepCycle: final / Resolution: 3.5→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12610 0 0 0 12610
Num. residues----1643
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5-3.630.34821330.31722561269499
3.63-3.770.33471330.304825182651100
3.77-3.940.35161340.291625572691100
3.94-4.150.34851360.276725742710100
4.15-4.410.26911330.237725422675100
4.41-4.750.27651350.21312554268999
4.75-5.230.27731350.21472560269599
5.23-5.980.25821360.22792583271999
5.98-7.530.27171370.22152610274799
7.53-46.430.2181410.16732678281999

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