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- PDB-6p9i: crystal structure of human anti staphylococcus aureus antibody ST... -

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Basic information

Entry
Database: PDB / ID: 6p9i
Titlecrystal structure of human anti staphylococcus aureus antibody STAU-399 Fab
Components
  • human anti staphylococcus aureus antibody STAU-399 Fab heavy chain
  • human anti staphylococcus aureus antibody STAU-399 Fab light chain
KeywordsIMMUNE SYSTEM / human antibody / Fab
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDong, J. / Crowe, J.E.
CitationJournal: Mbio / Year: 2019
Title: Human V H 1-69 Gene-Encoded Human Monoclonal Antibodies against Staphylococcus aureus IsdB Use at Least Three Distinct Modes of Binding To Inhibit Bacterial Growth and Pathogenesis.
Authors: Bennett, M.R. / Dong, J. / Bombardi, R.G. / Soto, C. / Parrington, H.M. / Nargi, R.S. / Schoeder, C.T. / Nagel, M.B. / Schey, K.L. / Meiler, J. / Skaar, E.P. / Crowe Jr., J.E.
History
DepositionJun 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: 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.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 6, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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: human anti staphylococcus aureus antibody STAU-399 Fab heavy chain
B: human anti staphylococcus aureus antibody STAU-399 Fab light chain
C: human anti staphylococcus aureus antibody STAU-399 Fab heavy chain
D: human anti staphylococcus aureus antibody STAU-399 Fab light chain


Theoretical massNumber of molelcules
Total (without water)94,5194
Polymers94,5194
Non-polymers00
Water5,405300
1
A: human anti staphylococcus aureus antibody STAU-399 Fab heavy chain
B: human anti staphylococcus aureus antibody STAU-399 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,2602
Polymers47,2602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-29 kcal/mol
Surface area19490 Å2
MethodPISA
2
C: human anti staphylococcus aureus antibody STAU-399 Fab heavy chain
D: human anti staphylococcus aureus antibody STAU-399 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,2602
Polymers47,2602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-28 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.590, 99.874, 93.877
Angle α, β, γ (deg.)90.00, 96.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody human anti staphylococcus aureus antibody STAU-399 Fab heavy chain


Mass: 24130.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody human anti staphylococcus aureus antibody STAU-399 Fab light chain


Mass: 23129.498 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 300 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 10% PEG 200, 18% PEG 8000, 0.1 M Bis-tris propane pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Oct 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.4→49.29 Å / Num. obs: 35657 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.581 / Num. unique obs: 5197

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRP

5jrp


Resolution: 2.4→45.71 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2434 1843 5.18 %
Rwork0.185 --
obs0.1879 35598 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6465 0 0 300 6765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026626
X-RAY DIFFRACTIONf_angle_d0.4829055
X-RAY DIFFRACTIONf_dihedral_angle_d5.4693909
X-RAY DIFFRACTIONf_chiral_restr0.0431037
X-RAY DIFFRACTIONf_plane_restr0.0041159
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.46490.35571430.3032587X-RAY DIFFRACTION100
2.4649-2.53740.32441530.25072585X-RAY DIFFRACTION100
2.5374-2.61930.28031330.23112579X-RAY DIFFRACTION100
2.6193-2.71290.28951410.21022582X-RAY DIFFRACTION100
2.7129-2.82150.28541420.20282588X-RAY DIFFRACTION100
2.8215-2.94990.28921520.21292582X-RAY DIFFRACTION100
2.9499-3.10540.27581200.20512616X-RAY DIFFRACTION100
3.1054-3.29990.24641440.1972585X-RAY DIFFRACTION100
3.2999-3.55460.22971350.18362610X-RAY DIFFRACTION100
3.5546-3.91220.27921470.17552588X-RAY DIFFRACTION100
3.9122-4.47790.2131480.14452609X-RAY DIFFRACTION100
4.4779-5.640.18621390.14792614X-RAY DIFFRACTION100
5.64-45.71810.19291460.18112630X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 8.4198 Å / Origin y: -10.6392 Å / Origin z: 22.4723 Å
111213212223313233
T0.2664 Å20.063 Å20.0273 Å2-0.2108 Å20.0022 Å2--0.2467 Å2
L0.2128 °20.0026 °20.0378 °2-0.1597 °20.02 °2--0.3648 °2
S0.0014 Å °0.024 Å °-0.001 Å °-0.0007 Å °0.0128 Å °-0.0512 Å °0.0531 Å °0.0637 Å °-0.0141 Å °
Refinement TLS groupSelection details: all

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