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- PDB-1l7i: Crystal Structure of the anti-ErbB2 Fab2C4 -

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Basic information

Entry
Database: PDB / ID: 1l7i
TitleCrystal Structure of the anti-ErbB2 Fab2C4
Components(chimera of Fab2C4: "humanized" murine monoclonal antibody) x 2
KeywordsIMMUNE SYSTEM / Ig domain / Fab fragment
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig-like domain-containing protein / :
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsVajdos, F.F. / Adams, C.W. / Breece, T.N. / Presta, L.G. / de Vos, A.M. / Sidhu, S.S.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis.
Authors: Vajdos, F.F. / Adams, C.W. / Breece, T.N. / Presta, L.G. / de Vos, A.M. / Sidhu, S.S.
History
DepositionMar 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence an appropriate sequence database reference was not available at the time of processing. ...sequence an appropriate sequence database reference was not available at the time of processing. Fab2C4 is a "humanized" murine monoclonal antibody, with the following residues corresponding to the human Ig sequence: L1-L23, L35-L49, L57-L88, L98-L214, H1-H25, H36-H49, H66-H68, H70, H72, H74-H94, H102-223. RESIDUES L24-L34, L50-L56, L89-L97, H26-H35, H50-H65, H69, H71, H73, H95-H102 CORRESPOND TO THE ORIGINAL MURINE SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: chimera of Fab2C4: "humanized" murine monoclonal antibody
H: chimera of Fab2C4: "humanized" murine monoclonal antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4154
Polymers47,2232
Non-polymers1922
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-44 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.966, 64.249, 79.445
Angle α, β, γ (deg.)90.00, 105.44, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a heterodimer of heavy and light chains.

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Components

#1: Antibody chimera of Fab2C4: "humanized" murine monoclonal antibody


Mass: 23548.152 Da / Num. of mol.: 1 / Fragment: light chain (residues 1-214)
Source method: isolated from a genetically manipulated source
Details: The chimera consists of the human Ig and the original murine sequence
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z3Y4
#2: Antibody chimera of Fab2C4: "humanized" murine monoclonal antibody


Mass: 23674.486 Da / Num. of mol.: 1 / Fragment: heavy chain (residues 1-216)
Source method: isolated from a genetically manipulated source
Details: The chimera consists of the human Ig and the original murine sequence
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7Z5W1
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.19 Å3/Da / Density % sol: 43.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 35%-45% saturated (NH4)2SO4, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122.5 mg/mlprotein1drop
235-45 %satammonium sulfate1reservoir
30.1 MTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 30, 2000
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. all: 36884 / Num. obs: 36884 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.2
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 1.4 / % possible all: 97.6
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 85734
Reflection shell
*PLUS
% possible obs: 97.6 % / Redundancy: 2.3 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNX2000.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→14.39 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1429863.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1833 5 %RANDOM
Rwork0.197 ---
all-36884 --
obs-36864 97.4 %-
Displacement parametersBiso mean: 24 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å20 Å2-2.36 Å2
2---2.3 Å20 Å2
3----1.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→14.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 10 392 3725
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it2.112
X-RAY DIFFRACTIONc_scangle_it3.092.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.338 271 4.5 %
Rwork0.27 5809 -
obs--96.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Rfactor Rwork: 0.27

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