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- PDB-6dwa: Structure of the 4497 Antibody Fab fragment bound to a Staphyloco... -

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Basic information

Entry
Database: PDB / ID: 6dwa
TitleStructure of the 4497 Antibody Fab fragment bound to a Staphylococcus aureus wall techoic acid analog
Components
  • 4497 Fab Heavy Chain
  • 4497 Fab Light Chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / wall teichoic acid / WTA / Staphylococcus aureus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-HD4
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.922 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: Data collection / Database references ...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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4497 Fab Light Chain
B: 4497 Fab Heavy Chain
H: 4497 Fab Heavy Chain
L: 4497 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,3546
Polymers104,4834
Non-polymers8712
Water7,692427
1
A: 4497 Fab Light Chain
B: 4497 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6773
Polymers52,2422
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-24 kcal/mol
Surface area18830 Å2
MethodPISA
2
H: 4497 Fab Heavy Chain
L: 4497 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6773
Polymers52,2422
Non-polymers4351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-25 kcal/mol
Surface area19410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.681, 114.443, 156.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody 4497 Fab Light Chain


Mass: 26485.666 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 4497 Fab Heavy Chain


Mass: 25755.895 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)
#3: 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.: 2 / Source method: obtained synthetically / Formula: C13H26NO13P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 0.16M Calcium Acetate, 0.08 M Sodium Cacodylate, pH 6.5, 14.4% PEG8000, and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 87337 / % possible obs: 99.5 % / Redundancy: 5.7 % / Biso Wilson estimate: 28.9 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.2
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 8494 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.7_648refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KVN

4kvn


Resolution: 1.922→42.563 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.18
RfactorNum. reflection% reflection
Rfree0.2352 4243 5.05 %
Rwork0.2069 --
obs0.2084 84098 95.87 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Bsol: 40.596 Å2 / ksol: 0.372 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.6531 Å20 Å2-0 Å2
2--1.1151 Å20 Å2
3----5.7682 Å2
Refinement stepCycle: LAST / Resolution: 1.922→42.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6585 0 56 427 7068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076844
X-RAY DIFFRACTIONf_angle_d1.0979311
X-RAY DIFFRACTIONf_dihedral_angle_d13.3052453
X-RAY DIFFRACTIONf_chiral_restr0.0731053
X-RAY DIFFRACTIONf_plane_restr0.0051193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9219-1.94370.3871030.28872236X-RAY DIFFRACTION81
1.9437-1.96660.31271260.26942356X-RAY DIFFRACTION87
1.9666-1.99060.30531160.26372462X-RAY DIFFRACTION88
1.9906-2.01580.32151470.24612417X-RAY DIFFRACTION89
2.0158-2.04230.2911380.24882450X-RAY DIFFRACTION90
2.0423-2.07030.2661370.24122444X-RAY DIFFRACTION91
2.0703-2.09990.27881210.23552538X-RAY DIFFRACTION92
2.0999-2.13120.2851350.22542620X-RAY DIFFRACTION94
2.1312-2.16450.28391310.21942592X-RAY DIFFRACTION94
2.1645-2.20.26111230.21232622X-RAY DIFFRACTION94
2.2-2.23790.24821360.21012586X-RAY DIFFRACTION95
2.2379-2.27860.241270.21222642X-RAY DIFFRACTION95
2.2786-2.32240.25041520.22632636X-RAY DIFFRACTION97
2.3224-2.36980.27661730.22272691X-RAY DIFFRACTION97
2.3698-2.42140.30431330.21292683X-RAY DIFFRACTION98
2.4214-2.47770.21451320.21032731X-RAY DIFFRACTION98
2.4777-2.53960.24671460.21192696X-RAY DIFFRACTION98
2.5396-2.60830.26851390.21832749X-RAY DIFFRACTION99
2.6083-2.6850.22551560.21572739X-RAY DIFFRACTION99
2.685-2.77170.27471330.20892777X-RAY DIFFRACTION99
2.7717-2.87070.25421490.21672753X-RAY DIFFRACTION100
2.8707-2.98560.23621650.20762738X-RAY DIFFRACTION100
2.9856-3.12150.24591670.20672774X-RAY DIFFRACTION100
3.1215-3.2860.2141460.19422788X-RAY DIFFRACTION100
3.286-3.49180.2171410.19122800X-RAY DIFFRACTION100
3.4918-3.76120.21791570.19242811X-RAY DIFFRACTION100
3.7612-4.13950.21361440.19042818X-RAY DIFFRACTION100
4.1395-4.73780.19461460.17192852X-RAY DIFFRACTION100
4.7378-5.96650.19581590.1962854X-RAY DIFFRACTION100
5.9665-42.57320.23561650.22783000X-RAY DIFFRACTION100

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