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- PDB-3vfg: Crystal structure of monoclonal antibody 3F8 Fab fragment that bi... -

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Basic information

Entry
Database: PDB / ID: 3vfg
TitleCrystal structure of monoclonal antibody 3F8 Fab fragment that binds to GD2 ganglioside
Components
  • 3F8 Heavy Chain
  • 3F8 Light Chain
KeywordsIMMUNE SYSTEM / Immunoglobulin / antibody / GD2 Ganglioside
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAhmed, M. / Goldgur, Y. / Cheung, N.-K.
CitationJournal: Plos One / Year: 2013
Title: In silico Driven Redesign of a Clinically Relevant Antibody for the Treatment of GD2 Positive Tumors.
Authors: Ahmed, M. / Goldgur, Y. / Hu, J. / Guo, H.F. / Cheung, N.K.
History
DepositionJan 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 29, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Jun 24, 2015Group: Structure summary
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 1.5Nov 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
L: 3F8 Light Chain
H: 3F8 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)46,6512
Polymers46,6512
Non-polymers00
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-23 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.028, 64.310, 57.241
Angle α, β, γ (deg.)90.00, 93.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody 3F8 Light Chain


Mass: 23250.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse)
#2: Antibody 3F8 Heavy Chain


Mass: 23400.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: MUS MUSCULUS (house mouse)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Hamptom Index D7, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 50590 / Num. obs: 49781 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3 / % possible all: 98.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AJU

2aju


Resolution: 1.65→28.58 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.134 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 2535 5.1 %RANDOM
Rwork0.17592 ---
obs0.17842 47192 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.259 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20.49 Å2
2--0.75 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 0 532 3796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.023339
X-RAY DIFFRACTIONr_bond_other_d0.0010.023074
X-RAY DIFFRACTIONr_angle_refined_deg2.0941.9454534
X-RAY DIFFRACTIONr_angle_other_deg0.9383.0037086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4095418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63724.109129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75715533
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1591513
X-RAY DIFFRACTIONr_chiral_restr0.1360.2513
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213743
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 184 -
Rwork0.227 3441 -
obs--97.39 %

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