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- PDB-3giz: Crystal structure of the Fab fragment of anti-CD20 antibody Ofatumumab -

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Basic information

Entry
Database: PDB / ID: 3giz
TitleCrystal structure of the Fab fragment of anti-CD20 antibody Ofatumumab
Components
  • Fab fragment of anti-CD20 antibody Ofatumumab, heavy chain
  • Fab fragment of anti-CD20 antibody Ofatumumab, light chain
KeywordsIMMUNE SYSTEM / CD20 / 2F2 / Ofatumumab / Hu-MaxCD20 / Fab / antibody / fully human antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDu, J. / Yang, H. / Ding, J.
CitationJournal: Mol.Immunol. / Year: 2009
Title: Structure of the Fab fragment of therapeutic antibody Ofatumumab provides insights into the recognition mechanism with CD20
Authors: Du, J. / Yang, H. / Guo, Y. / Ding, J.
History
DepositionMar 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 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: Fab fragment of anti-CD20 antibody Ofatumumab, light chain
H: Fab fragment of anti-CD20 antibody Ofatumumab, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0885
Polymers46,8922
Non-polymers1963
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-52 kcal/mol
Surface area19490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.330, 55.944, 79.780
Angle α, β, γ (deg.)90.00, 122.17, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-212-

ZN

21H-312-

HOH

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Components

#1: Antibody Fab fragment of anti-CD20 antibody Ofatumumab, light chain


Mass: 23174.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): ovary (CHO) cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1
#2: Antibody Fab fragment of anti-CD20 antibody Ofatumumab, heavy chain


Mass: 23717.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA3.1 / Cell line (production host): ovary (CHO) cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): K1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 0.2 M zinc acetate, 20% PEG3350, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 26208 / Num. obs: 26051 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2618 / Rsym value: 0.325 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1U6A

1u6a


Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.908 / SU B: 13.528 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24957 1288 5 %RANDOM
Rwork0.19477 ---
all0.19752 25899 --
obs0.19752 24611 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.506 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.17 Å2
2--1.2 Å20 Å2
3----1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3261 0 3 221 3485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223341
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.9534550
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.6524.074135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68215527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7961516
X-RAY DIFFRACTIONr_chiral_restr0.0930.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022536
X-RAY DIFFRACTIONr_nbd_refined0.1960.21341
X-RAY DIFFRACTIONr_nbtor_refined0.30.22179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2221
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.210
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2940.21
X-RAY DIFFRACTIONr_mcbond_it0.6961.52179
X-RAY DIFFRACTIONr_mcangle_it1.17523429
X-RAY DIFFRACTIONr_scbond_it1.56331352
X-RAY DIFFRACTIONr_scangle_it2.3184.51121
X-RAY DIFFRACTIONr_rigid_bond_restr1.14433531
X-RAY DIFFRACTIONr_sphericity_free3.9563224
X-RAY DIFFRACTIONr_sphericity_bonded1.33733261
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 94 -
Rwork0.239 1792 -
obs-1792 99.26 %

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