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- PDB-5d6c: Structure of 4497 Fab bound to synthetic wall teichoic acid fragment -

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Basic information

Entry
Database: PDB / ID: 5d6c
TitleStructure of 4497 Fab bound to synthetic wall teichoic acid fragment
Components(4497 antibody ...) x 2
KeywordsIMMUNE SYSTEM / Staphylococcus aureus wall teichoic acid antibody MRSA
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-57S / ACETATE ION
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLupardus, P.J. / Fong, R.
CitationJournal: Nature / Year: 2015
Title: Novel antibody-antibiotic conjugate eliminates intracellular S. aureus.
Authors: Lehar, S.M. / Pillow, T. / Xu, M. / Staben, L. / Kajihara, K.K. / Vandlen, R. / DePalatis, L. / Raab, H. / Hazenbos, W.L. / Morisaki, J.H. / Kim, J. / Park, S. / Darwish, M. / Lee, B.C. / ...Authors: Lehar, S.M. / Pillow, T. / Xu, M. / Staben, L. / Kajihara, K.K. / Vandlen, R. / DePalatis, L. / Raab, H. / Hazenbos, W.L. / Morisaki, J.H. / Kim, J. / Park, S. / Darwish, M. / Lee, B.C. / Hernandez, H. / Loyet, K.M. / Lupardus, P. / Fong, R. / Yan, D. / Chalouni, C. / Luis, E. / Khalfin, Y. / Plise, E. / Cheong, J. / Lyssikatos, J.P. / Strandh, M. / Koefoed, K. / Andersen, P.S. / Flygare, J.A. / Wah Tan, M. / Brown, E.J. / Mariathasan, S.
History
DepositionAug 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / 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 / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4497 antibody IgK (VL and CL)
B: 4497 antibody IgG1 (VH and CH1)
H: 4497 antibody IgG1 (VH and CH1)
L: 4497 antibody IgK (VL and CL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,76713
Polymers96,5264
Non-polymers1,2419
Water12,647702
1
A: 4497 antibody IgK (VL and CL)
B: 4497 antibody IgG1 (VH and CH1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7785
Polymers48,2632
Non-polymers5153
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-36 kcal/mol
Surface area18980 Å2
MethodPISA
2
H: 4497 antibody IgG1 (VH and CH1)
L: 4497 antibody IgK (VL and CL)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9888
Polymers48,2632
Non-polymers7266
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-54 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.707, 111.471, 158.412
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules ALBH

#1: Antibody 4497 antibody IgK (VL and CL)


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)
#2: Antibody 4497 antibody IgG1 (VH and CH1)


Mass: 23766.500 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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Sugars , 1 types, 2 molecules

#4: Sugar ChemComp-57S / 4-O-[2-acetamido-2-deoxy-beta-D-glucopyranosyl]-5-O-phosphono-D-ribitol


Type: D-saccharide / Mass: 435.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H26NO13P

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Non-polymers , 4 types, 709 molecules

#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ACT / ACETATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.08M sodium cacodylate pH 6.5, 0.16M calcium acetate, 14.4% PEG-8000, and 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 20024 / % possible obs: 99.9 % / Redundancy: 6 % / Biso Wilson estimate: 30.36 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 29.4
Reflection shellResolution: 1.72→1.78 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.839 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.4refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→33.64 Å / Cor.coef. Fo:Fc: 0.9525 / Cor.coef. Fo:Fc free: 0.9349 / SU R Cruickshank DPI: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.104 / SU Rfree Blow DPI: 0.104 / SU Rfree Cruickshank DPI: 0.102
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 6101 5.08 %RANDOM
Rwork0.2033 ---
obs0.205 -99.87 %-
Displacement parametersBiso mean: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1--5.9341 Å20 Å20 Å2
2--0.106 Å20 Å2
3---5.828 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: 1 / Resolution: 1.72→33.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6700 0 74 702 7476
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016942HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.139465HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2333SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes156HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1026HARMONIC5
X-RAY DIFFRACTIONt_it6942HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.01
X-RAY DIFFRACTIONt_other_torsion16.53
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion920SEMIHARMONIC5
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_contact8289SEMIHARMONIC4
LS refinement shellResolution: 1.72→1.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2665 439 5.06 %
Rwork0.2536 8237 -
all0.2543 8676 -
obs--99.87 %

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