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- PDB-1baf: 2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-... -

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Basic information

Entry
Database: PDB / ID: 1baf
Title2.9 ANGSTROMS RESOLUTION STRUCTURE OF AN ANTI-DINITROPHENYL-SPIN-LABEL MONOCLONAL ANTIBODY FAB FRAGMENT WITH BOUND HAPTEN
Components
  • IGG1-KAPPA AN02 FAB (HEAVY CHAIN)
  • IGG1-KAPPA AN02 FAB (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-NPP / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsLeahy, D.J. / Brunger, A.T. / Fox, R.O. / Hynes, T.R.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: 2.9 A resolution structure of an anti-dinitrophenyl-spin-label monoclonal antibody Fab fragment with bound hapten.
Authors: Brunger, A.T. / Leahy, D.J. / Hynes, T.R. / Fox, R.O.
#1: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization of an Anti-2,2,6, 6-Tetramethyl-1-Piperidinyloxy-Dinitrophenyl Monoclonal Antibody Fab Fragment with and without Bound Hapten
Authors: Leahy, D.J. / Hynes, T.R. / Mcconnell, H.M. / Fox, R.O.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988
Title: Sequences of 12 Monoclonal Anti-Dinitrophenyl Spin-Label Antibodies for NMR Studies
Authors: Leahy, D.J. / Rule, G.S. / Whittaker, M.M. / Mcconnell, H.M.
#3: Journal: Biochim.Biophys.Acta / Year: 1982
Title: Monoclonal Antibodies to a Nitroxide Lipid Hapten
Authors: Balakrishnan, K. / Hsu, F.J. / Hafeman, D.G. / Mcconnell, H.M.
History
DepositionJan 16, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: 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: IGG1-KAPPA AN02 FAB (LIGHT CHAIN)
H: IGG1-KAPPA AN02 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6133
Polymers47,2182
Non-polymers3951
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-27 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.230, 73.230, 373.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Atom site foot note1: CIS PROLINE - PRO L 8
2: CIS PROLINE - PRO L 95 RESIDUES TYR L 93 - PRO L 95 DISPLAYED UNINTERPRETABLE DENSITY AND ARE CONSIDERED DISORDERED IN THIS STRUCTURE.
3: CIS PROLINE - PRO L 141 / 4: CIS PROLINE - PRO H 101 / 5: CIS PROLINE - PRO H 149 / 6: CIS PROLINE - PRO H 151 / 7: CIS PROLINE - PRO H 191
8: RESIDUES LEU H 126 - ASN H 135 DISPLAYED UNINTERPRETABLE DENSITY AND ARE CONSIDERED DISORDERED IN THIS STRUCTURE.

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Components

#1: Antibody IGG1-KAPPA AN02 FAB (LIGHT CHAIN)


Mass: 23582.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 437099
#2: Antibody IGG1-KAPPA AN02 FAB (HEAVY CHAIN)


Mass: 23635.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1513182
#3: Chemical ChemComp-NPP / N-(2-AMINO-ETHYL)-4,6-DINITRO-N'-(2,2,6,6-TETRAMETHYL-1-OXY-PIPERIDIN-4-YL)-BENZENE-1,3-DIAMINE


Mass: 395.433 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H27N6O5
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: 3.06 Å3/Da / Density % sol: 59.83 %
Crystal grow
*PLUS
pH: 7.4 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlFab solution11
2150 mM12NaCl
310 mM12Na2PO4
40.02 %(w/v)12NaN3

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 12775 / Num. measured all: 70064 / Rmerge(I) obs: 0.14

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.9→8 Å / Rfactor Rwork: 0.195 / Rfactor obs: 0.195 / σ(F): 0
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 28 0 3342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
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_deg3.1
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 8 Å / σ(F): 0 / Rfactor all: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.1

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