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- PDB-6dwi: Structure of the 4462 Antibody Fab fragment bound to a Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 6dwi
TitleStructure of the 4462 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog
Components
  • 4462 Fab Heavy chain
  • 4462 Fab Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / wall teichoic acid / WTA / Staphylococcus aureus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION / Chem-HD4
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsFong, R. / Lupardus, P.J.
CitationJournal: MAbs / Year: 2018
Title: Structural investigation of human S. aureus-targeting antibodies that bind wall teichoic acid.
Authors: Fong, R. / Kajihara, K. / Chen, M. / Hotzel, I. / Mariathasan, S. / Hazenbos, W.L.W. / Lupardus, P.J.
History
DepositionJun 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4462 Fab Light Chain
B: 4462 Fab Heavy chain
C: 4462 Fab Light Chain
D: 4462 Fab Heavy chain
E: 4462 Fab Light Chain
F: 4462 Fab Heavy chain
G: 4462 Fab Light Chain
H: 4462 Fab Heavy chain
I: 4462 Fab Light Chain
J: 4462 Fab Heavy chain
K: 4462 Fab Light Chain
L: 4462 Fab Heavy chain
M: 4462 Fab Light Chain
N: 4462 Fab Heavy chain
O: 4462 Fab Light Chain
P: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)411,76329
Polymers409,43616
Non-polymers2,32713
Water13,295738
1
A: 4462 Fab Light Chain
B: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2504
Polymers51,1792
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-40 kcal/mol
Surface area19140 Å2
MethodPISA
2
C: 4462 Fab Light Chain
D: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6504
Polymers51,1792
Non-polymers4712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-36 kcal/mol
Surface area18890 Å2
MethodPISA
3
E: 4462 Fab Light Chain
F: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2153
Polymers51,1792
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-34 kcal/mol
Surface area18590 Å2
MethodPISA
4
G: 4462 Fab Light Chain
H: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9316
Polymers51,1792
Non-polymers7524
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-33 kcal/mol
Surface area18730 Å2
MethodPISA
5
I: 4462 Fab Light Chain
J: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7074
Polymers51,1792
Non-polymers5272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-24 kcal/mol
Surface area19140 Å2
MethodPISA
6
K: 4462 Fab Light Chain
L: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6153
Polymers51,1792
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-24 kcal/mol
Surface area19140 Å2
MethodPISA
7
M: 4462 Fab Light Chain
N: 4462 Fab Heavy chain


Theoretical massNumber of molelcules
Total (without water)51,1792
Polymers51,1792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3200 Å2
ΔGint-23 kcal/mol
Surface area18640 Å2
MethodPISA
8
O: 4462 Fab Light Chain
P: 4462 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2153
Polymers51,1792
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-37 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.573, 114.097, 128.301
Angle α, β, γ (deg.)90.00, 90.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Antibody , 2 types, 16 molecules ACEGIKMOBDFHJLNP

#1: Antibody
4462 Fab Light Chain


Mass: 25321.330 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
4462 Fab Heavy chain


Mass: 25858.113 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Sugars , 1 types, 4 molecules

#4: Sugar
ChemComp-HD4 / 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol / 4-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-1-O-phosphono-D-ribitol / 4-O-[2-acetamido-2-deoxy-beta-D-glucosyl]-1-O-phosphono-D-ribitol / 4-O-[2-acetamido-2-deoxy-D-glucosyl]-1-O-phosphono-D-ribitol / 4-O-[2-acetamido-2-deoxy-glucosyl]-1-O-phosphono-D-ribitol


Type: D-saccharide / Mass: 435.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H26NO13P

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Non-polymers , 4 types, 747 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 738 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Citric Acid, pH 3.5 containing 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→30 Å / Num. obs: 138384 / % possible obs: 99.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 52.85 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.3
Reflection shellResolution: 2.39→2.49 Å / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 13635 / % possible all: 98.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KVN

4kvn


Resolution: 2.39→29.89 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.429 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.407 / SU Rfree Blow DPI: 0.252 / SU Rfree Cruickshank DPI: 0.259
RfactorNum. reflection% reflectionSelection details
Rfree0.249 6978 5.04 %RANDOM
Rwork0.203 ---
obs0.206 138362 99 %-
Displacement parametersBiso mean: 45.27 Å2
Baniso -1Baniso -2Baniso -3
1-2.0516 Å20 Å22.973 Å2
2---1.4333 Å20 Å2
3----0.6183 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: 1 / Resolution: 2.39→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25289 0 143 738 26170
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126047HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2335482HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d8550SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes4343HARMONIC5
X-RAY DIFFRACTIONt_it26047HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.51
X-RAY DIFFRACTIONt_other_torsion18.62
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion3518SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact29235SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3353 489 5.16 %
Rwork0.2468 8988 -
all0.2512 9477 -
obs--91.79 %

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