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- PDB-1bbd: THREE DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A NEUTRALIZING... -

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Basic information

Entry
Database: PDB / ID: 1bbd
TitleTHREE DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A NEUTRALIZING ANTIBODY TO HUMAN RHINOVIRUS SEROTYPE 2
Components
  • IGG2A-KAPPA 8F5 FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 8F5 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
: / : / ENSMUSG00000076577 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsTormo, J. / Blaas, D. / Fita, I.
Citation
Journal: Protein Sci. / Year: 1992
Title: Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2.
Authors: Tormo, J. / Stadler, E. / Skern, T. / Auer, H. / Kanzler, O. / Betzel, C. / Blaas, D. / Fita, I.
#1: Journal: J.Biol.Chem. / Year: 1990
Title: Crystallization and Preliminary X-Ray Diffraction Studies of the Fab Fragment of a Neutralizing Monoclonal Antibody Directed Against Human Rhinovirus Serotype 2
Authors: Tormo, J. / Fita, I. / Kanzler, O. / Blaas, D.
History
DepositionMay 5, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 1.4Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 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: IGG2A-KAPPA 8F5 FAB (LIGHT CHAIN)
H: IGG2A-KAPPA 8F5 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1013
Polymers48,0052
Non-polymers961
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-38 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.700, 86.800, 128.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 101 / 3: CIS PROLINE - PRO L 147 / 4: RESIDUE ARG H 13 IS MISSING SIDE CHAIN ATOMS. / 5: CIS PROLINE - PRO H 152 / 6: CIS PROLINE - PRO H 154 / 7: CIS PROLINE - PRO H 194

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Components

#1: Antibody IGG2A-KAPPA 8F5 FAB (LIGHT CHAIN)


Mass: 24416.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 208622, UniProt: Q52L64*PLUS
#2: Antibody IGG2A-KAPPA 8F5 FAB (HEAVY CHAIN)


Mass: 23588.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 2072133
#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.: 5 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.8 Mammonium sulfate1reservoir
20.1 Mpotassium phosphate1reservoir
310 mg/mlprotein1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 15894 / % possible obs: 93.5 % / Observed criterion σ(F): 2.5 / Num. measured all: 74187 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.95 Å / % possible obs: 87.9 % / Num. unique obs: 2086 / Rmerge(I) obs: 0.196

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.8→7 Å /
RfactorNum. reflection
obs0.19 14494
Refinement stepCycle: LAST / Resolution: 2.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3332 0 5 5 3342
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0530.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0690.05
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_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.2250.15
X-RAY DIFFRACTIONp_singtor_nbd0.2450.5
X-RAY DIFFRACTIONp_multtor_nbd0.2930.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2990.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.13
X-RAY DIFFRACTIONp_staggered_tor24.415
X-RAY DIFFRACTIONp_orthonormal_tor18.520
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 7 Å / Num. reflection obs: 14494 / σ(F): 2.5 / Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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