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- PDB-4wcy: Fab fragment of mouse AZ130 monoclonal antibody -

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Basic information

Entry
Database: PDB / ID: 4wcy
TitleFab fragment of mouse AZ130 monoclonal antibody
Components
  • AZ130 Heavy chain
  • AZ130 Light chain
KeywordsIMMUNE SYSTEM / Monoclonal antibody / Epstein-Barr virus (EBV) / ZEBRA protein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFallecker, C. / Tarbouriech, N. / Habib, M. / Crepin, T. / Drouet, E.
CitationJournal: To Be Published
Title: Fab fragment of mouse AZ130 monoclonal antibody
Authors: Fallecker, C. / Tarbouriech, N. / Habib, M. / Crepin, T. / Drouet, E.
History
DepositionSep 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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 1.2Nov 13, 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
H: AZ130 Heavy chain
L: AZ130 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7346
Polymers47,3612
Non-polymers3724
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-40 kcal/mol
Surface area19370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.157, 68.825, 113.042
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody AZ130 Heavy chain


Mass: 23400.029 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody AZ130 Light chain


Mass: 23961.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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

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Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium sulfate 0.2 M, BIS-TRIS 0.1 M, Polyethylene glycol 3,350 25 %w/v

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 22, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2→58 Å / Num. all: 35076 / Num. obs: 34652 / % possible obs: 98.8 % / Redundancy: 4.83 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.09
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.09 % / % possible all: 91.6

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMAC5.8.0071refinement
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4K26

4k26


Resolution: 2→58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.625 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22354 1656 4.8 %RANDOM
Rwork0.17224 ---
obs0.17465 33000 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.831 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 2→58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3253 0 23 302 3578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.023381
X-RAY DIFFRACTIONr_bond_other_d0.0010.023065
X-RAY DIFFRACTIONr_angle_refined_deg1.5521.9534624
X-RAY DIFFRACTIONr_angle_other_deg0.76737116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2555432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.46325.075134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26615524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5641510
X-RAY DIFFRACTIONr_chiral_restr0.1160.2532
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213824
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02734
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_it1.8641.8491713
X-RAY DIFFRACTIONr_mcbond_other1.8611.8461712
X-RAY DIFFRACTIONr_mcangle_it2.7132.752138
X-RAY DIFFRACTIONr_mcangle_other2.7142.7532139
X-RAY DIFFRACTIONr_scbond_it3.3682.1841668
X-RAY DIFFRACTIONr_scbond_other3.3362.1771664
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9953.1132477
X-RAY DIFFRACTIONr_long_range_B_refined6.75215.7843754
X-RAY DIFFRACTIONr_long_range_B_other6.64715.4893658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 115 -
Rwork0.222 2169 -
obs--89.36 %

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