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- PDB-12e8: 2E8 FAB FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 1200000000
Title2E8 FAB FRAGMENT
Components
  • IGG1-KAPPA 2E8 FAB (HEAVY CHAIN)
  • IGG1-KAPPA 2E8 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRupp, B. / Trakhanov, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of a monoclonal 2E8 Fab antibody fragment specific for the low-density lipoprotein-receptor binding region of apolipoprotein E refined at 1.9 A.
Authors: Trakhanov, S. / Parkin, S. / Raffai, R. / Milne, R. / Newhouse, Y.M. / Weisgraber, K.H. / Rupp, B.
History
DepositionMar 14, 1998Processing site: BNL
Revision 1.0Aug 5, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 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: IGG1-KAPPA 2E8 FAB (LIGHT CHAIN)
H: IGG1-KAPPA 2E8 FAB (HEAVY CHAIN)
M: IGG1-KAPPA 2E8 FAB (LIGHT CHAIN)
P: IGG1-KAPPA 2E8 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)94,8394
Polymers94,8394
Non-polymers00
Water13,818767
1
L: IGG1-KAPPA 2E8 FAB (LIGHT CHAIN)
H: IGG1-KAPPA 2E8 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,4202
Polymers47,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-21 kcal/mol
Surface area19980 Å2
MethodPISA, PQS
2
M: IGG1-KAPPA 2E8 FAB (LIGHT CHAIN)
P: IGG1-KAPPA 2E8 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,4202
Polymers47,4202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3650 Å2
ΔGint-23 kcal/mol
Surface area19820 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)66.560, 65.570, 103.220
Angle α, β, γ (deg.)90.00, 97.04, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.981807, 0.162499, 0.098229), (0.160259, 0.986609, -0.030336), (-0.101843, -0.014042, -0.994701)96.4331, -2.1854, 2.2392
2given(-0.990419, 0.137999, 0.005096), (0.136567, 0.98428, -0.111995), (-0.020471, -0.110226, -0.993696)99.4533, 0.0349, 2.457
3given(-0.997869, 0.0608, 0.023663), (0.060892, 0.998139, 0.003195), (-0.023425, 0.004629, -0.999715)101.545, -1.3038, -1.0226
4given(-0.990478, 0.137268, -0.010491), (0.137523, 0.983072, -0.121069), (-0.006306, -0.121359, -0.992589)100.0034, 0.4615, 2.1677

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Components

#1: Antibody IGG1-KAPPA 2E8 FAB (LIGHT CHAIN)


Mass: 23540.990 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 2E8 HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C / References: GenBank: 10121892
#2: Antibody IGG1-KAPPA 2E8 FAB (HEAVY CHAIN)


Mass: 23878.586 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 2E8 HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C / References: PIR: S49220
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 767 / 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.

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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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growpH: 5.6
Details: 23% PEG 4000 (W/V), 0.10 M SODIUM CITRATE, AND 0.2 M AMMONIUM ACETATE (PH 5.6). CRYSTALS (0.2 X 0.2 X 0.5 MM) WERE OBTAINED IN 4-6 WEEKS.
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
14 mg/mlprotein1drop
223 %(w/v)PEG40001reservoir
30.10 Msodium citrate1reservoir
40.2 Mammonium acetate1reservoirpH5.6

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: ADSC / Detector: AREA DETECTOR / Date: May 1, 1996 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.85 Å / Num. obs: 63078 / % possible obs: 84 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.071 / Net I/σ(I): 6
Reflection shellResolution: 1.85→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.27 / % possible all: 82
Reflection
*PLUS
Num. measured all: 237795

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Processing

Software
NameVersionClassification
UCSDDATA PROCESSING SOFTWAREdata collection
UCSDDATA PROCESSING SOFTWAREdata reduction
X-PLOR3.851model building
X-PLOR3.851refinement
UCSDdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 6FAB AND 1FLR

6fab

1flr


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0
Details: BULK SOLVENT MODEL USED. THE CONNECTING LOOP BETWEEN BETA STRANDS B AND C IN THE CH1 DOMAIN IS POORLY DEFINED IN THE STRUCTURE. ATTEMPTS TO IMPROVE THE LOOP H123-H133 USING VARIOUS NCS ...Details: BULK SOLVENT MODEL USED. THE CONNECTING LOOP BETWEEN BETA STRANDS B AND C IN THE CH1 DOMAIN IS POORLY DEFINED IN THE STRUCTURE. ATTEMPTS TO IMPROVE THE LOOP H123-H133 USING VARIOUS NCS AVERAGING SCHEMES AS WELL AS AUTOMATED REBUILDING AND REFINEMENT WITH ARP DID NOT IMPROVE THIS REGION. HOWEVER, USING ARP THE TRACING OF CH BETA STRANDS B-E WAS CONFIRMED INDEPENDENT OF ANY STARTING MODEL. THE CONNECTING LOOP BETWEEN BETA STRANDS B AND C IN THE CH1 DOMAIN IS POORLY DEFINED IN THE STRUCTURE. ATTEMPTS TO IMPROVE THE LOOP H123-H133 USING VARIOUS NCS AVERAGING SCHEMES AS WELL AS AUTOMATED REBUILDING AND REFINEMENT WITH ARP DID NOT IMPROVE THIS REGION. HOWEVER, USING ARP THE TRACING OF CH BETA STRANDS B-E WAS CONFIRMED INDEPENDENT OF ANY STARTING MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1143 1.9 %RANDOM
Rwork0.221 ---
obs0.221 58785 84.4 %-
Displacement parametersBiso mean: 16.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-6 Å
Luzzati sigma a0.33 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6662 0 0 767 7429
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.211.5
X-RAY DIFFRACTIONx_mcangle_it3.112
X-RAY DIFFRACTIONx_scbond_it3.512
X-RAY DIFFRACTIONx_scangle_it4.842.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 187 2.1 %
Rwork0.309 8652 -
obs--76.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WAT
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_deg28.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55

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