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- PDB-1ce1: 1.9A STRUCTURE OF THE THERAPEUTIC ANTIBODY CAMPATH-1H FAB IN COMP... -

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Basic information

Entry
Database: PDB / ID: 1ce1
Title1.9A STRUCTURE OF THE THERAPEUTIC ANTIBODY CAMPATH-1H FAB IN COMPLEX WITH A SYNTHETIC PEPTIDE ANTIGEN
Components
  • PROTEIN (CAMPATH-1H:HEAVY CHAIN)
  • PROTEIN (CAMPATH-1H:LIGHT CHAIN)
  • PROTEIN (PEPTIDE ANTIGEN)
KeywordsIMMUNE SYSTEM / THERAPEUTIC / ANTIBODY / CD52
Function / homology
Function and homology information


: / Immunoglobulin/major histocompatibility complex, conserved site / 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 / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Hepatitis B virus receptor binding protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJames, L.C. / Hale, G. / Waldmann, H. / Bloomer, A.C.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: 1.9 A structure of the therapeutic antibody CAMPATH-1H fab in complex with a synthetic peptide antigen.
Authors: James, L.C. / Hale, G. / Waldmann, H. / Bloomer, A.C.
History
DepositionMar 12, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 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: PROTEIN (CAMPATH-1H:LIGHT CHAIN)
H: PROTEIN (CAMPATH-1H:HEAVY CHAIN)
P: PROTEIN (PEPTIDE ANTIGEN)


Theoretical massNumber of molelcules
Total (without water)47,5753
Polymers47,5753
Non-polymers00
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area18880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.846, 60.672, 152.908
Angle α, β, γ (deg.)90.00, 89.72, 89.85
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody PROTEIN (CAMPATH-1H:LIGHT CHAIN)


Mass: 23306.965 Da / Num. of mol.: 1 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 243868
#2: Antibody PROTEIN (CAMPATH-1H:HEAVY CHAIN)


Mass: 23547.422 Da / Num. of mol.: 1 / Fragment: FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: GenBank: 243866, UniProt: Q6PYX1*PLUS
#3: Protein/peptide PROTEIN (PEPTIDE ANTIGEN)


Mass: 720.685 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SYNTHETIC PEPTIDE;
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 23 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMheptapeptide1reservoir
220 %PEG100001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorDate: Feb 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 40254 / % possible obs: 98.8 % / Redundancy: 3 % / Rmerge(I) obs: 0.054
Reflection shellHighest resolution: 1.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.0269 / % possible all: 95.1
Reflection
*PLUS
Rmerge(I) obs: 0.062
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / % possible obs: 95.1 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→6 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.27 -10 %RANDOM
Rwork0.22 ---
obs0.22 40254 98 %-
Refinement stepCycle: LAST / Resolution: 1.9→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 0 377 3720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d0.025
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Rfactor obs: 0.208 / Rfactor Rfree: 0.265
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.6

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