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- PDB-6p9j: crystal structure of human anti staphylococcus aureus antibody ST... -

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Basic information

Entry
Database: PDB / ID: 6p9j
Titlecrystal structure of human anti staphylococcus aureus antibody STAU-229 Fab
Components
  • human anti staphylococcus aureus antibody STAU-229 Fab heavy chain
  • human anti staphylococcus aureus antibody STAU-229 Fab light chain
KeywordsIMMUNE SYSTEM / human antibody / Fab
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: human anti staphylococcus aureus antibody STAU-229 Fab heavy chain
L: human anti staphylococcus aureus antibody STAU-229 Fab light chain
A: human anti staphylococcus aureus antibody STAU-229 Fab heavy chain
B: human anti staphylococcus aureus antibody STAU-229 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,0975
Polymers94,9344
Non-polymers1631
Water1,44180
1
H: human anti staphylococcus aureus antibody STAU-229 Fab heavy chain
L: human anti staphylococcus aureus antibody STAU-229 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6303
Polymers47,4672
Non-polymers1631
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-24 kcal/mol
Surface area18560 Å2
MethodPISA
2
A: human anti staphylococcus aureus antibody STAU-229 Fab heavy chain
B: human anti staphylococcus aureus antibody STAU-229 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,4672
Polymers47,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-28 kcal/mol
Surface area18950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.827, 66.039, 112.329
Angle α, β, γ (deg.)90.00, 96.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody human anti staphylococcus aureus antibody STAU-229 Fab heavy chain


Mass: 24709.773 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-229 Fab light chain


Mass: 22757.057 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: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M ammonium acetate, 0.1 M Bis-tris pH 5.5, 17% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.2→48.92 Å / Num. obs: 43034 / % possible obs: 99.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.32 Å / Rmerge(I) obs: 0.788 / Num. unique obs: 6144

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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: 2.2→42.628 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.31
RfactorNum. reflection% reflection
Rfree0.267 2141 4.99 %
Rwork0.2181 --
obs0.2206 42873 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→42.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6185 0 11 80 6276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056354
X-RAY DIFFRACTIONf_angle_d0.7228676
X-RAY DIFFRACTIONf_dihedral_angle_d4.4673744
X-RAY DIFFRACTIONf_chiral_restr0.047982
X-RAY DIFFRACTIONf_plane_restr0.0051109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1968-2.24790.4241410.34982587X-RAY DIFFRACTION95
2.2479-2.30410.37881480.33162665X-RAY DIFFRACTION100
2.3041-2.36640.41211360.31862711X-RAY DIFFRACTION99
2.3664-2.4360.36751220.29722716X-RAY DIFFRACTION100
2.436-2.51460.32561490.29062718X-RAY DIFFRACTION100
2.5146-2.60450.38491420.27762683X-RAY DIFFRACTION100
2.6045-2.70880.34411470.28422698X-RAY DIFFRACTION100
2.7088-2.8320.3271450.27952729X-RAY DIFFRACTION100
2.832-2.98130.35391330.26962696X-RAY DIFFRACTION100
2.9813-3.1680.34311430.25812738X-RAY DIFFRACTION100
3.168-3.41250.30971460.23622723X-RAY DIFFRACTION100
3.4125-3.75580.23831520.2082718X-RAY DIFFRACTION100
3.7558-4.29880.20931350.16692769X-RAY DIFFRACTION100
4.2988-5.41430.15951580.13452756X-RAY DIFFRACTION100
5.4143-42.63590.20951440.17442825X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.6773 Å / Origin y: 22.9764 Å / Origin z: 27.033 Å
111213212223313233
T0.2662 Å2-0.0238 Å2-0.0166 Å2-0.5518 Å20.0624 Å2--0.301 Å2
L0.0661 °20.0818 °2-0.0579 °2-0.2825 °20.1741 °2--0.2514 °2
S-0.0065 Å °-0.0002 Å °-0.0263 Å °-0.0258 Å °-0.0024 Å °-0.0056 Å °-0.034 Å °-0.0136 Å °0.0083 Å °
Refinement TLS groupSelection details: all

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