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- PDB-7qxd: Recognition of Staphylococcus aureus wall teichoic acid analogue ... -

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Basic information

Entry
Database: PDB / ID: 7qxd
TitleRecognition of Staphylococcus aureus wall teichoic acid analogue SA475 (compound 2) by Fab4497
Components(Antibody Fab 4497 ...) x 2
KeywordsCARBOHYDRATE / Antibody / Fab fragment / teichoic acid analogue
Function / homologyChem-G5F / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.649 Å
AuthorsSoriano-Maldonado, P. / van Raaij, M.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)BFU2017-82207-P Spain
CitationJournal: Acs Cent.Sci. / Year: 2022
Title: Antibody Recognition of Different Staphylococcus aureus Wall Teichoic Acid Glycoforms.
Authors: Di Carluccio, C. / Soriano-Maldonado, P. / Berni, F. / de Haas, C.J.C. / Temming, A.R. / Hendriks, A. / Ali, S. / Molinaro, A. / Silipo, A. / van Sorge, N.M. / van Raaij, M.J. / Codee, J.D.C. / Marchetti, R.
History
DepositionJan 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HHH: Antibody Fab 4497 heavy chain
LLL: Antibody Fab 4497 light chain
KKK: Antibody Fab 4497 heavy chain
MMM: Antibody Fab 4497 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,80311
Polymers98,7544
Non-polymers2,0507
Water14,736818
1
HHH: Antibody Fab 4497 heavy chain
LLL: Antibody Fab 4497 light chain
hetero molecules


  • defined by author&software
  • 50.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,3495
Polymers49,3772
Non-polymers9723
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-33 kcal/mol
Surface area19620 Å2
MethodPISA
2
KKK: Antibody Fab 4497 heavy chain
MMM: Antibody Fab 4497 light chain
hetero molecules


  • defined by author&software
  • 50.5 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)50,4556
Polymers49,3772
Non-polymers1,0784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-39 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.392, 113.371, 154.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11HHH
21KKK
32LLL
42MMM

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUPROPROHHHA1 - 2161 - 216
221GLUGLUPROPROKKKC1 - 2161 - 216
332ASPASPGLUGLULLLB1 - 2191 - 219
442ASPASPGLUGLUMMMD1 - 2191 - 219

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

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Antibody , 2 types, 4 molecules HHHKKKLLLMMM

#1: Antibody Antibody Fab 4497 heavy chain


Mass: 24880.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Antibody Fab 4497 light chain


Mass: 24496.275 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 825 molecules

#3: Chemical ChemComp-G5F / [(2~{S},3~{S},4~{R})-4-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-5-[[(2~{S},3~{R})-2,3-bis(oxidanyl)butoxy]-oxidanyl-phosphoryl]oxy-2,3-bis(oxidanyl)pentyl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate


Mass: 783.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H47NO24P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 10 mM 2-(N-morpholino)ethanesulfonic acid-NaOH pH 6.2, 0.25 M sodium chloride, 20% (w/v) poly-ethylene glycol 4000, 10% (v/v) glycerol, 200 mM magnesium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97933 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.649→91.41 Å / Num. obs: 127285 / % possible obs: 92.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.4 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.049 / Rrim(I) all: 0.092 / Net I/σ(I): 12
Reflection shellResolution: 1.649→1.74 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 19760 / CC1/2: 0.661 / Rpim(I) all: 0.67 / Rrim(I) all: 1.247 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSJan 31, 2020data reduction
Aimless0.7.4data scaling
REFMAC5.8.0258phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 5D6C

5d6c


Resolution: 1.649→90.016 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.002 / SU ML: 0.064 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2018 6287 4.947 %
Rwork0.1747 120810 -
all0.176 --
obs-127097 92.962 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.699 Å2
Baniso -1Baniso -2Baniso -3
1-0.747 Å2-0 Å20 Å2
2---0.59 Å2-0 Å2
3----0.157 Å2
Refinement stepCycle: LAST / Resolution: 1.649→90.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6636 0 125 818 7579
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0156364
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.6499471
X-RAY DIFFRACTIONr_angle_other_deg1.3941.57714730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.675875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18422.593324
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.049151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.831535
X-RAY DIFFRACTIONr_chiral_restr0.0690.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027843
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021595
X-RAY DIFFRACTIONr_nbd_refined0.1960.21025
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.25942
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23329
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2602
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2120.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2310.213
X-RAY DIFFRACTIONr_nbd_other0.180.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1750.242
X-RAY DIFFRACTIONr_mcbond_it2.1662.4783475
X-RAY DIFFRACTIONr_mcbond_other2.1612.4773474
X-RAY DIFFRACTIONr_mcangle_it3.2393.6994337
X-RAY DIFFRACTIONr_mcangle_other3.2383.74338
X-RAY DIFFRACTIONr_scbond_it3.152.8053481
X-RAY DIFFRACTIONr_scbond_other3.1232.83474
X-RAY DIFFRACTIONr_scangle_it4.8594.0415127
X-RAY DIFFRACTIONr_scangle_other4.8324.0325116
X-RAY DIFFRACTIONr_lrange_it6.6429.8147552
X-RAY DIFFRACTIONr_lrange_other6.50329.2327348
X-RAY DIFFRACTIONr_ncsr_local_group_10.0920.056315
X-RAY DIFFRACTIONr_ncsr_local_group_20.0910.056739
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11HHHX-RAY DIFFRACTIONLocal ncs0.092240.05009
12KKKX-RAY DIFFRACTIONLocal ncs0.092240.05009
23LLLX-RAY DIFFRACTIONLocal ncs0.090740.05008
24MMMX-RAY DIFFRACTIONLocal ncs0.090740.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.649-1.7380.2999620.29218773X-RAY DIFFRACTION99.9899
1.738-1.8440.2659530.23417754X-RAY DIFFRACTION100
1.844-1.9710.2445060.20910051X-RAY DIFFRACTION60.0717
1.971-2.1290.2138270.18415599X-RAY DIFFRACTION99.9817
2.129-2.3320.2126730.17412496X-RAY DIFFRACTION86.9126
2.332-2.6070.2126780.16513060X-RAY DIFFRACTION99.9927
2.607-3.0090.1976140.16611559X-RAY DIFFRACTION100
3.009-3.6850.1925120.1659862X-RAY DIFFRACTION99.9422
3.685-5.2070.1583510.1397168X-RAY DIFFRACTION92.5985
5.207-90.0160.1762100.1794452X-RAY DIFFRACTION99.8287

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