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- PDB-7t87: CRYSTAL STRUCTURE OF LEUKOCIDIN AB/CENTYRIN S17/FAB 214F COMPLEX -

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Basic information

Entry
Database: PDB / ID: 7t87
TitleCRYSTAL STRUCTURE OF LEUKOCIDIN AB/CENTYRIN S17/FAB 214F COMPLEX
Components
  • Antibody Fab B214 Heavy Chain
  • Antibody Fab B214 Light Chain
  • Centyrin S17
  • Leukocidin A
  • Leukocidin B
KeywordsTOXIN / Staphylcoccus aureus / lukocidin AB / Centyrin / Fab
Function / homologyImmunoglobulins / 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 Å
Model detailsCrystal Structure of FN3tt, a Fibronectin-like Domain from T. tengcongensis
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 13, 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 B
B: Leukocidin A
L: Antibody Fab B214 Light Chain
H: Antibody Fab B214 Heavy Chain
C: Centyrin S17


Theoretical massNumber of molelcules
Total (without water)133,3925
Polymers133,3925
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.980, 173.740, 174.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Leukocidin B


Mass: 35625.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcaceae (Staphylococcus group)
#2: Protein Leukocidin A


Mass: 38655.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Staphylococcaceae (Staphylococcus group)
#3: Antibody Antibody Fab B214 Light Chain


Mass: 23129.779 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#4: Antibody Antibody Fab B214 Heavy Chain


Mass: 25070.887 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse)
#5: Protein Centyrin S17


Mass: 10910.249 Da / Num. of mol.: 1 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1 M MES pH 6.5, 26% PEG 3350, 0.2 M diammonium tartrate

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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 11, 2011 / 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→49.158 Å / Num. obs: 27208 / % possible obs: 95 % / Redundancy: 3.912 % / Biso Wilson estimate: 63.786 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.15 / Rrim(I) all: 0.17 / Χ2: 0.984 / Net I/σ(I): 10.51 / Num. measured all: 106449 / Scaling rejects: 11
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
3-3.083.8220.9931.937215208618880.6161.13190.5
3.08-3.163.9980.8372.457889202619730.7050.94997.4
3.16-3.253.9240.6123.137483196019070.810.69497.3
3.25-3.353.8960.5043.757347195418860.860.57496.5
3.35-3.463.7760.4054.76514185317250.9120.46493.1
3.46-3.593.890.2856.446846182417600.9430.32496.5
3.59-3.723.7990.2417.386397174916840.960.27596.3
3.72-3.874.0650.1968.896646169516350.9730.22296.5
3.87-4.053.9960.15810.376229162215590.9830.17996.1
4.05-4.243.9590.11212.915899155114900.990.12796.1
4.24-4.473.9220.0915.365460148513920.9930.10393.7
4.47-4.743.8810.07716.875119138813190.9940.08895
4.74-5.073.9270.07217.714960131912630.9960.08295.8
5.07-5.484.0770.06918.114868125911940.9970.07894.8
5.48-64.0360.07916.674278111910600.9940.0994.7
6-6.713.8320.07516.75370610499670.9950.08692.2
6.71-7.753.8240.06318.6233159198670.9950.07294.3
7.75-9.494.0370.04325.3729837927390.9980.04993.3
9.49-13.423.7020.03829.1821216235730.9980.04492
13.42-49.1583.590.03828.8311743703270.9980.04488.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4tw1

4tw1


Resolution: 3→49.158 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2473 1360 5 %
Rwork0.1957 25837 -
obs0.1983 27197 94.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.5 Å2 / Biso mean: 63.5825 Å2 / Biso min: 12.81 Å2
Refinement stepCycle: final / Resolution: 3→49.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8641 0 0 0 8641
Num. residues----1100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0038857
X-RAY DIFFRACTIONf_angle_d0.52612018
X-RAY DIFFRACTIONf_chiral_restr0.0421294
X-RAY DIFFRACTIONf_plane_restr0.0041546
X-RAY DIFFRACTIONf_dihedral_angle_d13.1375243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.0002-3.10740.38791300.3241247492
3.1074-3.23180.3481370.2781259597
3.2318-3.37890.31811360.2638258196
3.3789-3.5570.30431330.2295254094
3.557-3.77970.28221390.2008262397
3.7797-4.07140.2361360.1896259496
4.0714-4.48090.20681360.1578258795
4.4809-5.12870.21081370.146260695
5.1287-6.45930.20511360.178258394
6.4593-49.1580.21341400.1898265493

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