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- PDB-1bey: ANTIBODY TO CAMPATH-1H HUMANIZED FAB -

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Basic information

Entry
Database: PDB / ID: 1bey
TitleANTIBODY TO CAMPATH-1H HUMANIZED FAB
Components(CAMPATH-1H ANTIBODY) x 2
KeywordsANTIBODY / FAB / CAMPATH-1H / CD52
Function / homology
Function and homology information


immunoglobulin complex / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Ig-like domain-containing protein / IGH@ protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsCheetham, G.M.T. / Hale, G. / Waldmann, H. / Bloomer, A.C.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Crystal structures of a rat anti-CD52 (CAMPATH-1) therapeutic antibody Fab fragment and its humanized counterpart.
Authors: Cheetham, G.M. / Hale, G. / Waldmann, H. / Bloomer, A.C.
History
DepositionMay 18, 1998Processing site: BNL
Revision 1.0Jan 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: 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: CAMPATH-1H ANTIBODY
H: CAMPATH-1H ANTIBODY


Theoretical massNumber of molelcules
Total (without water)47,0152
Polymers47,0152
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-20 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.060, 80.060, 347.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody CAMPATH-1H ANTIBODY


Mass: 23596.271 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: HYBRIDOMA CULTURE SUPERNATANT / Source: (natural) Homo sapiens (human) / References: GenBank: 243868, UniProt: Q6GMX0*PLUS
#2: Antibody CAMPATH-1H ANTIBODY


Mass: 23418.307 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Details: HYBRIDOMA CULTURE SUPERNATANT / Source: (natural) Homo sapiens (human) / References: GenBank: 243866, UniProt: Q6GMX6*PLUS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 58 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 %PEG40001reservoir
30.2 Mimidazole1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1992 / Details: MIRRORS
RadiationMonochromator: MONOCHROMATOR / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.25→20 Å / Num. obs: 10139 / % possible obs: 92 % / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.11 / Net I/σ(I): 8
Reflection shellResolution: 3.25→3.42 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.204 / % possible all: 67
Reflection shell
*PLUS
% possible obs: 86.6 % / Rmerge(I) obs: 0.227

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
CNSrefinement
CCP4(ROTAVATA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 7FAB (CON) 1FDL (VAR)

7fab

1fdl


Resolution: 3.25→6 Å / Rfactor Rfree error: 0.014 / Isotropic thermal model: GROUPED, UNRESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.306 462 5 %RANDOM
Rwork0.214 ---
obs0.214 8437 90.9 %-
Displacement parametersBiso mean: 54.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.59 Å0.39 Å
Luzzati d res low-6 Å
Luzzati sigma a0.9 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3.25→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3247 0 0 0 3247
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.23
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.25→3.35 Å / Rfactor Rfree error: 0.059 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.337 32 3.5 %
Rwork0.321 604 -
obs--68.6 %
Xplor fileSerial no: 1 / Param file: CNS_TOPPAR:PROTEIN_REP.PA / Topol file: CNS_TOPPAR:PROTEIN.TOP
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.229 / Rfactor Rfree: 0.309
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
LS refinement shell
*PLUS
Rfactor obs: 0.321

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