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- PDB-4kaq: Structure of rituximab Fab -

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Basic information

Entry
Database: PDB / ID: 4kaq
TitleStructure of rituximab Fab
Components
  • Rituximab heavy chain
  • Rituximab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: To be Published
Title: Crystal structure of rituximab
Authors: Bzymek, K.P. / Williams, J.C.
History
DepositionApr 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 20, 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 2.2Oct 30, 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: Rituximab light chain
H: Rituximab heavy chain


Theoretical massNumber of molelcules
Total (without water)46,7952
Polymers46,7952
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-27 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.650, 93.930, 144.390
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-408-

HOH

21H-334-

HOH

31H-365-

HOH

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Components

#1: Antibody Rituximab light chain


Mass: 23078.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Commercially available as Rituxin / Source: (gene. exp.) Homo sapiens, Mus musculus
#2: Antibody Rituximab heavy chain


Mass: 23716.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Commercially available as Rituxin / Source: (gene. exp.) Homo sapiens, Mus musculus
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22% PEG 3350, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 8, 2013
RadiationMonochromator: Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→30.32 Å / Num. all: 15014 / Num. obs: 14891 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 22.4
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 6.3 / % possible all: 92.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: dev_1320)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSL

2osl


Resolution: 2.48→30.32 Å / SU ML: 0.3 / σ(F): 2 / σ(I): 2 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2303 745 5 %random
Rwork0.1796 ---
all0.1822 15014 --
obs0.1822 14889 99.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.48→30.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 0 252 3498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033358
X-RAY DIFFRACTIONf_angle_d0.8084579
X-RAY DIFFRACTIONf_dihedral_angle_d12.0251193
X-RAY DIFFRACTIONf_chiral_restr0.05514
X-RAY DIFFRACTIONf_plane_restr0.004583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4805-2.67190.28861430.20912724X-RAY DIFFRACTION97
2.6719-2.94050.28241490.21192824X-RAY DIFFRACTION100
2.9405-3.36560.2731470.19542796X-RAY DIFFRACTION100
3.3656-4.23840.22081500.16712841X-RAY DIFFRACTION100
4.2384-30.32730.16381560.15272959X-RAY DIFFRACTION100

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