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- PDB-1a5f: FAB FRAGMENT OF A MONOCLONAL ANTI-E-SELECTIN ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1a5f
TitleFAB FRAGMENT OF A MONOCLONAL ANTI-E-SELECTIN ANTIBODY
Components
  • MONOCLONAL ANTI-E-SELECTIN 7A9 ANTIBODY (HEAVY CHAIN)
  • MONOCLONAL ANTI-E-SELECTIN 7A9 ANTIBODY (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / FAB / ANTIBODY / ANTI-E-SELECTIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRodriguez-Romero, A. / Almog, O. / Tordova, M. / Randhawa, Z.
CitationJournal: J.Biol.Chem. / Year: 1998
Title: Primary and tertiary structures of the Fab fragment of a monoclonal anti-E-selectin 7A9 antibody that inhibits neutrophil attachment to endothelial cells.
Authors: Rodriguez-Romero, A. / Almog, O. / Tordova, M. / Randhawa, Z. / Gilliland, G.L.
History
DepositionFeb 16, 1998Processing site: BNL
Revision 1.0Apr 20, 1999Provider: 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 / 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 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: MONOCLONAL ANTI-E-SELECTIN 7A9 ANTIBODY (LIGHT CHAIN)
H: MONOCLONAL ANTI-E-SELECTIN 7A9 ANTIBODY (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)47,3682
Polymers47,3682
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-20 kcal/mol
Surface area20040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.460, 83.790, 132.450
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 MONOCLONAL ANTI-E-SELECTIN 7A9 ANTIBODY (LIGHT CHAIN)


Mass: 24286.814 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: SP-20 FUSION MOUSE-MOUSE HYBRIDOMA / References: GenBank: 208622
#2: Antibody MONOCLONAL ANTI-E-SELECTIN 7A9 ANTIBODY (HEAVY CHAIN)


Mass: 23080.766 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: SP-20 FUSION MOUSE-MOUSE HYBRIDOMA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.6 Å3/Da / Density % sol: 53 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.6 mg/mlprotein1drop
210 mMHEPES-HCl1drop
30.2 Mammonium sulfate1reservoir
40.1 Msodium cacodylate1reservoir
520 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: May 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / Num. obs: 10993 / % possible obs: 86.5 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 4.6
Reflection
*PLUS
Num. measured all: 42928 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
XENGENdata collection
SCALEK(XENGEN)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
SCALEK(XENGEN)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BBD

1bbd


Resolution: 2.8→7 Å / Isotropic thermal model: GROUP / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.195 --
obs0.195 8184 86.6 %
Displacement parametersBiso mean: 14.6 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 0 10 3264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.95
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
LS refinement shellResolution: 2.8→2.96 Å / Total num. of bins used: 6 /
RfactorNum. reflection
Rwork0.255 389
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.H2OTOPOL.H2O
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 9420
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.95

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