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- PDB-6dwc: Structure of the apo 4497 antibody Fab fragment -

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Basic information

Entry
Database: PDB / ID: 6dwc
TitleStructure of the apo 4497 antibody Fab fragment
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 / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)104,6937
Polymers104,4834
Non-polymers2103
Water11,223623
1
A: 4497 Fab Light Chain
B: 4497 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3013
Polymers52,2422
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-24 kcal/mol
Surface area19360 Å2
MethodPISA
2
H: 4497 Fab Heavy Chain
L: 4497 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3934
Polymers52,2422
Non-polymers1512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-26 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.360, 109.670, 156.750
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 623 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
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: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→156.75 Å / Num. obs: 52278 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 46.73 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 30.6
Reflection shellResolution: 2.27→2.39 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.9 / Num. unique obs: 7553 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KVN

4kvn


Resolution: 2.27→89.86 Å / Cor.coef. Fo:Fc: 0.9292 / Cor.coef. Fo:Fc free: 0.9208 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.258 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.185
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 2645 5.12 %RANDOM
Rwork0.184 ---
obs0.1857 51637 99.09 %-
Displacement parametersBiso mean: 42.66 Å2
Baniso -1Baniso -2Baniso -3
1--13.4973 Å20 Å20 Å2
2--8.1066 Å20 Å2
3---5.3906 Å2
Refine analyzeLuzzati coordinate error obs: 0.258 Å
Refinement stepCycle: 1 / Resolution: 2.27→89.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 14 623 7299
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016842HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.179314HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2297SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes154HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1010HARMONIC5
X-RAY DIFFRACTIONt_it6842HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion17.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion895SEMIHARMONIC5
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_contact8013SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.33 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3681 189 5.39 %
Rwork0.2692 3315 -
all0.2742 3504 -
obs--99.09 %

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