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- PDB-1opg: OPG2 FAB FRAGMENT -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1opg
TitleOPG2 FAB FRAGMENT
Components
  • OPG2 FAB (HEAVY CHAIN)
  • OPG2 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN / CELL ADHESION MOLECULE
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / positive regulation of phagocytosis / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / cytoplasm
Similarity search - Function
: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...: / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKodandapani, R. / Veerapandian, B. / Ely, K.R.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: Crystal structure of the OPG2 Fab. An antireceptor antibody that mimics an RGD cell adhesion site.
Authors: Kodandapani, R. / Veerapandian, B. / Kunicki, T.J. / Ely, K.R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1992
Title: Crystallization of Opg2 Fab Fragment: A Fibrinogen Mimic with Specificity for the Platelet Glycoprotein
Authors: Celikel, R. / Williamson, M.M. / Kunicki, T.J. / Ely, K.R.
History
DepositionApr 28, 1995Processing site: BNL
Revision 1.0Jul 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: OPG2 FAB (LIGHT CHAIN)
H: OPG2 FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)48,0582
Polymers48,0582
Non-polymers00
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-30 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.100, 83.800, 53.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 95 / 3: CIS PROLINE - PRO L 141 / 4: CIS PROLINE - PRO H 159 / 5: CIS PROLINE - PRO H 161

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Components

#1: Antibody OPG2 FAB (LIGHT CHAIN)


Mass: 23549.811 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLATELET
#2: Antibody OPG2 FAB (HEAVY CHAIN)


Mass: 24508.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: PLATELET / References: UniProt: P01868
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 488 / 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

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.53 %
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, hanging drop
Details: Celikel, R., (1993) Acta Crystallogr.,Sect.D, 49, 421.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 %(w/v)PEG10001reservoir
20.02 Mimidazole malate1reservoir
30.16 M1reservoirNaCl

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Data collection

DetectorDate: Mar 12, 1992
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 28703 / % possible obs: 99 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 89211 / Rmerge(I) obs: 0.044

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Processing

Software
NameVersionClassification
HOWARDdata collection
A.J.data collection
NILSENdata collection
C.& XUONG N-H METHOD.data collection
PROLSQrefinement
XENGEN(HOWARDdata reduction
NIELSENdata reduction
XUONG)data reduction
RefinementResolution: 2→10 Å / σ(F): 3 /
RfactorNum. reflection
obs0.16 22609
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3478 0 0 488 3966
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0170.02
X-RAY DIFFRACTIONp_angle_d0.0630.045
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.035
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0160.02
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.220.3
X-RAY DIFFRACTIONp_multtor_nbd0.2680.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2560.3
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.95
X-RAY DIFFRACTIONp_staggered_tor24.320
X-RAY DIFFRACTIONp_orthonormal_tor21.320
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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