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- PDB-1j05: The crystal structure of anti-carcinoembryonic antigen monoclonal... -

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Basic information

Entry
Database: PDB / ID: 1j05
TitleThe crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment
Components
  • anti-CEA mAb T84.66, heavy chain
  • anti-CEA mAb T84.66, light chain
KeywordsIMMUNE SYSTEM / Immunoglobulin
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / blood microparticle / adaptive immune response / immune response / extracellular space
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ig kappa chain V-III region PC 3741/TEPC 111 / Anti-myosin immunoglobulin heavy chain variable region
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKondo, H. / Nishimura, Y. / Shiroishi, M. / Asano, R. / Noro, N. / Tsumoto, K. / Kumagai, I.
CitationJournal: To be Published
Title: The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment
Authors: Kondo, H. / Nishimura, Y. / Shiroishi, M. / Asano, R. / Noro, N. / Tsumoto, K. / Kumagai, I.
History
DepositionNov 1, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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
L: anti-CEA mAb T84.66, light chain
H: anti-CEA mAb T84.66, heavy chain
A: anti-CEA mAb T84.66, light chain
B: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0688
Polymers50,6944
Non-polymers3744
Water4,612256
1
L: anti-CEA mAb T84.66, light chain
H: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5344
Polymers25,3472
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-17 kcal/mol
Surface area10600 Å2
MethodPISA
2
A: anti-CEA mAb T84.66, light chain
B: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5344
Polymers25,3472
Non-polymers1872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2020 Å2
ΔGint-17 kcal/mol
Surface area10410 Å2
MethodPISA
3
A: anti-CEA mAb T84.66, light chain
B: anti-CEA mAb T84.66, heavy chain
hetero molecules

L: anti-CEA mAb T84.66, light chain
H: anti-CEA mAb T84.66, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0688
Polymers50,6944
Non-polymers3744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_647-x+1,y-1/2,-z+21
Buried area5150 Å2
ΔGint-39 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.774, 75.033, 63.105
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assemblies are formed between chain L and H and between A and B.

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Components

#1: Antibody anti-CEA mAb T84.66, light chain / T84.66 antibody


Mass: 12113.562 Da / Num. of mol.: 2 / Fragment: Fv fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01660
#2: Antibody anti-CEA mAb T84.66, heavy chain / T84.66 antibody


Mass: 13233.598 Da / Num. of mol.: 2 / Fragment: Fv fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9JL85
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2.7 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Na, K Phosphate, Na Hepes, Glycerol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→23.25 Å / Num. all: 91647 / Num. obs: 91647 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 6.7
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 2.2 / Num. unique all: 13262 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
SHELXL-97refinement
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→5 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.217 8909 random
Rwork0.185 --
all0.19 91647 -
obs0.185 88978 -
Refinement stepCycle: LAST / Resolution: 1.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3562 0 22 256 3840

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