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- PDB-1for: STRUCTURE DETERMINATION OF AN FAB FRAGMENT THAT NEUTRALIZES HUMAN... -

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Basic information

Entry
Database: PDB / ID: 1for
TitleSTRUCTURE DETERMINATION OF AN FAB FRAGMENT THAT NEUTRALIZES HUMAN RHINOVIRUS AND ANALYSIS OF THE FAB-VIRUS COMPLEX
Components
  • IGG2A-KAPPA 17-IA FAB (HEAVY CHAIN)
  • IGG2A-KAPPA 17-IA FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.75 Å
AuthorsSmith, T.J. / Liu, H.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Structure determination of an Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex.
Authors: Liu, H. / Smith, T.J. / Lee, W.M. / Mosser, A.G. / Rueckert, R.R. / Olson, N.H. / Cheng, R.H. / Baker, T.S.
#1: Journal: J.Virol. / Year: 1993
Title: Structure of Human Rhinovirus Complexed with Fab Fragments from a Neutralizing Antibody
Authors: Smith, T.J. / Olson, N.H. / Cheng, R.H. / Liu, H. / Chase, E.S. / Lee, W.M. / Leippe, D.M. / Mosser, A.G. / Rueckert, R.R. / Baker, T.S.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Structure of a Human Rhinovirus-Bivalently Bound Antibody Complex: Implications for Viral Neutralization and Antibody Flexibility
Authors: Smith, T.J. / Olson, N.H. / Cheng, R.H. / Chase, E.S. / Baker, T.S.
History
DepositionMay 24, 1994Processing site: BNL
Revision 1.0Sep 30, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
L: IGG2A-KAPPA 17-IA FAB (LIGHT CHAIN)
H: IGG2A-KAPPA 17-IA FAB (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,3512
Polymers46,3512
Non-polymers00
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-24 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.800, 97.300, 129.500
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

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Components

#1: Antibody IGG2A-KAPPA 17-IA FAB (LIGHT CHAIN)


Mass: 23052.541 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: EMBL: X79906
#2: Antibody IGG2A-KAPPA 17-IA FAB (HEAVY CHAIN)


Mass: 23298.002 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: PIR: S38950
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 %PEG80001drop
23 mMsodium azide1drop
30.1 Msodium phosphate1drop
410 mMTris-HCl1drop
54 mg/mlFab1drop

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 12367 / Num. measured all: 44321 / Rmerge(I) obs: 0.051

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.75→6 Å / Rfactor Rwork: 0.174 / Rfactor obs: 0.174 / σ(F): 2
Refinement stepCycle: LAST / Resolution: 2.75→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 0 157 3416
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_deg1.574
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 1.574

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