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- PDB-1ad0: FAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY A5B7 -

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Basic information

Entry
Database: PDB / ID: 1ad0
TitleFAB FRAGMENT OF ENGINEERED HUMAN MONOCLONAL ANTIBODY A5B7
Components
  • ANTIBODY A5B7 (HEAVY CHAIN)
  • ANTIBODY A5B7 (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: 2.5 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 19, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIBODY A5B7 (LIGHT CHAIN)
B: ANTIBODY A5B7 (HEAVY CHAIN)
C: ANTIBODY A5B7 (LIGHT CHAIN)
D: ANTIBODY A5B7 (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)94,0274
Polymers94,0274
Non-polymers00
Water2,342130
1
A: ANTIBODY A5B7 (LIGHT CHAIN)
B: ANTIBODY A5B7 (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,0132
Polymers47,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area18970 Å2
MethodPISA
2
C: ANTIBODY A5B7 (LIGHT CHAIN)
D: ANTIBODY A5B7 (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,0132
Polymers47,0132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-27 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.310, 66.270, 81.380
Angle α, β, γ (deg.)69.88, 82.48, 71.34
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody ANTIBODY A5B7 (LIGHT CHAIN)


Mass: 23182.686 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
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: 243868
#2: Antibody ANTIBODY A5B7 (HEAVY CHAIN)


Mass: 23830.668 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 43 %
Crystal growpH: 6
Details: PEG6000/400 CACL2, BUFFERED AT PH6 WITH 40MM BIS-TRIS, pH 6.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 %PEG60001reservoir
2400 mM1reservoirCaCl2
340 mMBis-Tris1reservoir
420 mMBis-Tris1drop
510 mg/mlprotain1drop

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorDetector: IMAGE PLATE / Date: Nov 1, 1995 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 29480 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 33.3 Å2 / Rsym value: 0.054 / Net I/σ(I): 12.2
Reflection shellResolution: 2.5→2.69 Å / Mean I/σ(I) obs: 3.8 / Rsym value: 0.179 / % possible all: 94
Reflection
*PLUS
Num. measured all: 49216 / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.179

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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 1CLO

1clo


Resolution: 2.5→15 Å / Rfactor Rfree error: 0.007 / 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
Rfree0.262 1493 5.1 %RANDOM
Rwork0.209 ---
obs0.209 29380 94.9 %-
Displacement parametersBiso mean: 22.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-10 Å
Luzzati sigma a0.4 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 0 130 130
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.391 161 4.4 %
Rwork0.294 3476 -
obs--93.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
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_deg27.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24

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