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

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Basic information

Entry
Database: PDB / ID: 7qxc
TitleRecognition of Staphylococcus aureus wall teichoic acid analogue SA533 (compound 1) by Fab4461
Components
  • Fab 4461 heavy chain
  • Fab 4461 light chain
KeywordsCARBOHYDRATE / Antibody / Fab fragment / teichoic acid analogue
Function / homologyChem-3CX / Chem-G6N / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.452 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 / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
HHH: Fab 4461 heavy chain
LLL: Fab 4461 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0508
Polymers49,6052
Non-polymers1,4456
Water7,638424
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.191, 65.448, 74.338
Angle α, β, γ (deg.)90.000, 112.899, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 2 molecules HHHLLL

#1: Antibody Fab 4461 heavy chain


Mass: 25147.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody Fab 4461 light chain


Mass: 24458.096 Da / Num. of mol.: 1
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 , 4 types, 430 molecules

#3: Chemical ChemComp-3CX / (2S)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid


Mass: 237.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO4S
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-G6N / [(2~{S},3~{S},4~{R})-4-[(2~{R},3~{R},4~{R},5~{S},6~{R})-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2,3-bis(oxidanyl)-5-[oxidanyl-[(2~{R})-2-oxidanylpropoxy]phosphoryl]oxy-pentyl] [(2~{R},3~{S},4~{S})-2,3,4,5-tetrakis(oxidanyl)pentyl] hydrogen phosphate


Mass: 783.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H47NO24P2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 10 mM Tris-HCl; 250 mM sodium chloride; 12.9 % w/v polyethylene glycol 20,000; 150 mM CAPSO pH 9.5; 6 % v/v polyethylene glycol 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.45→53.51 Å / Num. obs: 87656 / % possible obs: 96.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 21.8 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.028 / Rpim(I) all: 0.027 / Rrim(I) all: 0.039 / Net I/σ(I): 16.4
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10648 / CC1/2: 0.608 / Rpim(I) all: 0.406 / Rrim(I) all: 0.593 / % possible all: 80.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSJanuary 2020data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: separate constant and variable domains of PDB entry 5I1D

5i1d


Resolution: 1.452→53.51 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.231 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1999 4368 4.987 %
Rwork0.1743 83220 -
all0.176 --
obs-87588 96.54 %
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: 23.016 Å2
Baniso -1Baniso -2Baniso -3
1--0.415 Å20 Å2-0.061 Å2
2--0.101 Å2-0 Å2
3---0.269 Å2
Refinement stepCycle: LAST / Resolution: 1.452→53.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3317 0 88 424 3829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133489
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153183
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.6524738
X-RAY DIFFRACTIONr_angle_other_deg1.3521.5787374
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74223.032155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90815540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1321514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2461
X-RAY DIFFRACTIONr_chiral_restr_other0.0290.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023906
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02782
X-RAY DIFFRACTIONr_nbd_refined0.1970.2495
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22885
X-RAY DIFFRACTIONr_nbtor_refined0.1630.21653
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21815
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2302
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.28
X-RAY DIFFRACTIONr_nbd_other0.1210.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2310.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0840.21
X-RAY DIFFRACTIONr_mcbond_it1.9432.1991739
X-RAY DIFFRACTIONr_mcbond_other1.942.1971738
X-RAY DIFFRACTIONr_mcangle_it3.2013.2912169
X-RAY DIFFRACTIONr_mcangle_other3.23.2932170
X-RAY DIFFRACTIONr_scbond_it2.6132.5161750
X-RAY DIFFRACTIONr_scbond_other2.6132.5181751
X-RAY DIFFRACTIONr_scangle_it4.083.6262568
X-RAY DIFFRACTIONr_scangle_other4.0793.6282569
X-RAY DIFFRACTIONr_lrange_it6.35627.1053741
X-RAY DIFFRACTIONr_lrange_other6.30226.5623654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.452-1.530.3425290.33510122X-RAY DIFFRACTION80.7934
1.53-1.6230.2555940.24611849X-RAY DIFFRACTION99.5679
1.623-1.7350.2175870.19511088X-RAY DIFFRACTION99.5396
1.735-1.8740.2095300.18210342X-RAY DIFFRACTION99.5604
1.874-2.0530.214910.1779492X-RAY DIFFRACTION99.4719
2.053-2.2950.1994470.1738627X-RAY DIFFRACTION99.5284
2.295-2.6490.2064030.1627645X-RAY DIFFRACTION99.4194
2.649-3.2420.1993620.1666354X-RAY DIFFRACTION98.3597
3.242-4.5760.1642340.154920X-RAY DIFFRACTION97.3923
4.576-53.510.191900.1692764X-RAY DIFFRACTION98.3683

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