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- PDB-3nfs: Crystal structure the Fab fragment of therapeutic antibody daclizumab -

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Basic information

Entry
Database: PDB / ID: 3nfs
TitleCrystal structure the Fab fragment of therapeutic antibody daclizumab
Components
  • Heavy chain of Fab fragment of daclizumab
  • Light chain of Fab fragment of daclizumab
KeywordsIMMUNE SYSTEM / IL-2Ra / CD25 / Daclizumab / Zenapax / therapeutic antibody
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYang, H. / Wang, J. / Du, J. / Zhong, C. / Guo, Y. / Ding, J.
CitationJournal: Cell Res. / Year: 2010
Title: Structural basis of immunosuppression by the therapeutic antibody daclizumab
Authors: Yang, H. / Wang, J. / Du, J. / Zhong, C. / Zhang, D. / Guo, H. / Guo, Y. / Ding, J.
History
DepositionJun 10, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2013Group: Database references
Revision 1.3Nov 1, 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 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Heavy chain of Fab fragment of daclizumab
H: Light chain of Fab fragment of daclizumab


Theoretical massNumber of molelcules
Total (without water)46,1692
Polymers46,1692
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-23 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.866, 67.866, 205.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody Heavy chain of Fab fragment of daclizumab


Mass: 23134.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: purchased from Roche, expressed in a mammalian expression system
#2: Antibody Light chain of Fab fragment of daclizumab


Mass: 23034.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: purchased from Roche, expressed in a mammalian expression system
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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.1M ammonium sulfate, 2% PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Dec 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 15582 / % possible obs: 98.3 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 3.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 1.9 / Num. unique all: 1490 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GIZ

3giz


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / Occupancy max: 1 / Occupancy min: 1 / SU B: 30.624 / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.275 777 5.1 %RANDOM
Rwork0.225 ---
obs0.227 15305 98.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.74 Å2 / Biso mean: 48.78 Å2 / Biso min: 29.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2---0.82 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3203 0 0 0 3203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223282
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9524470
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.55824.524126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20815523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3881510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022466
X-RAY DIFFRACTIONr_nbd_refined0.2120.21321
X-RAY DIFFRACTIONr_nbtor_refined0.30.22169
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.23
X-RAY DIFFRACTIONr_mcbond_it1.2991.52137
X-RAY DIFFRACTIONr_mcangle_it2.2123400
X-RAY DIFFRACTIONr_scbond_it2.25831311
X-RAY DIFFRACTIONr_scangle_it3.2024.51070
X-RAY DIFFRACTIONr_rigid_bond_restr2.13833448
X-RAY DIFFRACTIONr_sphericity_free1.9933102
X-RAY DIFFRACTIONr_sphericity_bonded0.87733203
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 52 -
Rwork0.303 1045 -
all-1097 -
obs--100 %

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