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- PDB-1ad9: IGG-FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY CTM01 -

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Basic information

Entry
Database: PDB / ID: 1ad9
TitleIGG-FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY CTM01
Components
  • IGG CTM01 FAB (HEAVY CHAIN)
  • IGG CTM01 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / FAB FRAGMENT
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBanfield, M.J. / Brady, R.L.
CitationJournal: Proteins / Year: 1997
Title: VL:VH domain rotations in engineered antibodies: crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs.
Authors: Banfield, M.J. / King, D.J. / Mountain, A. / Brady, R.L.
History
DepositionFeb 24, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG CTM01 FAB (LIGHT CHAIN)
H: IGG CTM01 FAB (HEAVY CHAIN)
A: IGG CTM01 FAB (LIGHT CHAIN)
B: IGG CTM01 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0395
Polymers95,9434
Non-polymers961
Water27015
1
L: IGG CTM01 FAB (LIGHT CHAIN)
H: IGG CTM01 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,9722
Polymers47,9722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-29 kcal/mol
Surface area19860 Å2
MethodPISA
2
A: IGG CTM01 FAB (LIGHT CHAIN)
B: IGG CTM01 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0683
Polymers47,9722
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-43 kcal/mol
Surface area19900 Å2
MethodPISA
3
A: IGG CTM01 FAB (LIGHT CHAIN)
B: IGG CTM01 FAB (HEAVY CHAIN)
hetero molecules

L: IGG CTM01 FAB (LIGHT CHAIN)
H: IGG CTM01 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)96,0395
Polymers95,9434
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area7930 Å2
ΔGint-72 kcal/mol
Surface area39150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.390, 104.630, 119.380
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 IGG CTM01 FAB (LIGHT CHAIN)


Mass: 24161.998 Da / Num. of mol.: 2 / Fragment: CTM01
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): NSO CELLS / Production host: Mus musculus (house mouse) / References: GenBank: 468243
#2: Antibody IGG CTM01 FAB (HEAVY CHAIN)


Mass: 23809.568 Da / Num. of mol.: 2 / Fragment: CTM01
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): NSO CELLS / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAMINO ACIDS ARE NUMBERED ACCORDING TO THE KABAT NUMBERING SYSTEM FOR ANTIBODIES (KABAT, E.A., WU, T. ...AMINO ACIDS ARE NUMBERED ACCORDING TO THE KABAT NUMBERING SYSTEM FOR ANTIBODIES (KABAT, E.A., WU, T.T., REID-MILLER, M., PERRY, H.M. & GOTTESMAN, K.S. SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST , 4TH ED., NATIONAL INSTITUTES OF HEALTH, BETHESDA , MD. 1987.

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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: 2.5 Å3/Da / Density % sol: 45.6 %
Crystal growpH: 7.6
Details: 13-18% PEG4000/200-250MM LISO4, BUFFERED AT PH7.6 WITH 100MM TRIS
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMbis-Tris1drop
210 mg/mlprotein1drop
313-18 %PEG40001reservoir
4200-250 mM1reservoirLiSO4
5100 mMTris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 1, 1996 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 25776 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 34.5 Å2 / Rsym value: 0.105 / Net I/σ(I): 17.2
Reflection shellResolution: 2.8→3.02 Å / Mean I/σ(I) obs: 5.3 / Rsym value: 0.377 / % possible all: 99.9
Reflection
*PLUS
Num. measured all: 143861 / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.377

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AD0

1ad0


Resolution: 2.8→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1302 5.1 %RANDOM
Rwork0.233 ---
obs0.233 25502 99.8 %-
Displacement parametersBiso mean: 36.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.35 Å
Luzzati d res low-10 Å
Luzzati sigma a0.52 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.8→15 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 5 15 20
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.12
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.8→2.93 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.407 148 4.8 %
Rwork0.347 2952 -
obs--98.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2SO4.PARSO4.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.12

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