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- PDB-1b2w: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF A HUMANIZED AND... -

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Basic information

Entry
Database: PDB / ID: 1b2w
TitleCOMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF A HUMANIZED AND A CHIMERIC FAB OF AN ANTI-GAMMA-INTERFERON ANTIBODY
Components
  • PROTEIN (ANTIBODY (HEAVY CHAIN))
  • PROTEIN (ANTIBODY (LIGHT CHAIN))
KeywordsIMMUNE SYSTEM / ANTIBODY ENGINEERING / HUMANIZED AND CHIMERIC ANTIBODY / FAB / THREE-DIMENSIONAL STRYCTURE / GAMMA-INTERFERON
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsFan, Z. / Shan, L. / Goldsteen, B.Z. / Guddat, L.W. / Thakur, A. / Landolfi, N.F. / Co, M.S. / Vasquez, M. / Queen, C. / Ramsland, P.A. / Edmundson, A.B.
CitationJournal: J.Mol.Recog. / Year: 1999
Title: Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody.
Authors: Fan, Z.C. / Shan, L. / Goldsteen, B.Z. / Guddat, L.W. / Thakur, A. / Landolfi, N.F. / Co, M.S. / Vasquez, M. / Queen, C. / Ramsland, P.A. / Edmundson, A.B.
History
DepositionDec 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
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 2.1Aug 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PROTEIN (ANTIBODY (LIGHT CHAIN))
H: PROTEIN (ANTIBODY (HEAVY CHAIN))


Theoretical massNumber of molelcules
Total (without water)47,2322
Polymers47,2322
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-28 kcal/mol
Surface area19110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.100, 74.600, 104.300
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 PROTEIN (ANTIBODY (LIGHT CHAIN)) / IMMUNOGLOBULIN


Mass: 23430.879 Da / Num. of mol.: 1 / Fragment: V DOMAIN AND C DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens
#2: Antibody PROTEIN (ANTIBODY (HEAVY CHAIN)) / IMMUNOGLOBULIN


Mass: 23800.799 Da / Num. of mol.: 1 / Fragment: V DOMAIN AND C DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens

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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: 2.85 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.2
Details: 6.6% PEG 8000(W/V), IN 0.05 M NACL AND 0.05% SODIUM AZIDE., pH 6.2
Components of the solutions
IDNameCrystal-IDSol-ID
16.6% PEG 8000(W/V)12
20.05 M NACL12
30.05% SODIUM AZIDE12
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18-20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
135-45 mg/mlprotein1drop
26.6 %(w/v)PEG80001reservoir
30.05 M1reservoirNaCl
40.05 %sodium azide1reservoir

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jul 1, 1994
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.79→20 Å / Num. obs: 11491 / % possible obs: 81.7 % / Redundancy: 2.2 % / Biso Wilson estimate: 38.8 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 8.3
Reflection shellResolution: 2.79→2.96 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1 / Rsym value: 0.41 / % possible all: 0.28
Reflection
*PLUS
% possible obs: 67.2 %

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Processing

Software
NameVersionClassification
X-GENdata reduction
X-PLORmodel building
X-PLOR3.8refinement
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFB

1dfb


Resolution: 2.9→8 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.33 897 10 %RANDOM
Rwork0.188 ---
obs-9440 67.6 %-
Displacement parametersBiso mean: 30 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3325 0 0 0 3325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.36
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.052 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.37 51 3.6 %
Rwork0.26 372 -
obs--29.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PCA.PARPCA.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.331
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.36

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