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- PDB-2igf: CRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WI... -

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Basic information

Entry
Database: PDB / ID: 2igf
TitleCRYSTAL STRUCTURES OF AN ANTIBODY TO A PEPTIDE AND ITS COMPLEX WITH PEPTIDE ANTIGEN AT 2.8 ANGSTROMS
Components
  • IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
  • IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
  • PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)
KeywordsIMMUNOGLOBULIN
Function / homology
Function and homology information


oxygen carrier activity / iron ion binding
Similarity search - Function
Haemerythrin / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / : / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Immunoglobulins / Immunoglobulin-like ...Haemerythrin / Hemerythrin, metal-binding domain / Haemerythrin, iron-binding site / Hemerythrin-like superfamily / : / Hemerythrin family signature. / Hemerythrin-like / Hemerythrin HHE cation binding domain / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / : / Myohemerythrin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsStanfield, R.L. / Wilson, I.A.
Citation
Journal: Science / Year: 1990
Title: Crystal structures of an antibody to a peptide and its complex with peptide antigen at 2.8 A.
Authors: Stanfield, R.L. / Fieser, T.M. / Lerner, R.A. / Wilson, I.A.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Preliminary Crystallographic Data and Primary Sequence for Anti-Peptide Fab' B13I2 and its Complex with the C-Helix Peptide from Myohemerythrin
Authors: Stura, E.A. / Stanfield, R.L. / Fieser, T.M. / Balderas, R.S. / Smith, L.R. / Lerner, R.A. / Wilson, I.A.
History
DepositionMar 21, 1991Processing site: BNL
Revision 1.0Apr 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
H: IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
P: PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3894
Polymers50,1683
Non-polymers2211
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-32 kcal/mol
Surface area20030 Å2
MethodPISA
2
L: IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
H: IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
P: PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)
hetero molecules

L: IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)
H: IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)
P: PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7798
Polymers100,3366
Non-polymers4422
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area13310 Å2
ΔGint-70 kcal/mol
Surface area37090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.500, 142.500, 101.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Atom site foot note1: RESIDUES 8, 95, 141 OF THE *L* CHAIN AND 149, 151 OF THE *H* CHAIN ARE CIS PROLINES.
2: NAG 600 IS LINKED TO ASN L 26.

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Components

#1: Antibody IGG1-KAPPA B13I2 FAB (LIGHT CHAIN)


Mass: 24148.803 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: PC4203
#2: Antibody IGG1-KAPPA B13I2 FAB (HEAVY CHAIN)


Mass: 23807.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: A/J / References: PIR: S38864
#3: Protein/peptide PEPTIDE (RESIDUES 69-87 OF MYOHEMERYTHRIN)


Mass: 2211.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
References: UniProt: P02247
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has protein modificationY
Sequence detailsTHE FAB' FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M. ...THE FAB' FRAGMENT IS NUMBERED BY THE CONVENTION OF E.KABAT (E.A.KABAT,T.T.WU,M.REID-MILLER,H.M.PERRY,K.S.GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 4TH ED., (1987), NATIONAL INSTITUTE OF HEALTH,BETHESDA,MD.).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal grow
*PLUS
pH: 5.75 / Method: vapor diffusion, sitting drop
Details: taken from Stura, E.A. et al(1989). J. Biol. Chem., 264, 15721-15725.
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-ID
18 mg/mlprotein1drop
2mg/ml19-mer peptide1drop
3Mmonobasic sodium phosphate1reservoir
4Mdibasic potassium phosphate1reservoir

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Data collection

Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 26851 / Observed criterion σ(I): 2 / Num. measured all: 77906 / Rmerge(I) obs: 0.142

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementResolution: 2.8→8 Å / Rfactor Rwork: 0.22
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3422 0 14 0 3436
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg3.98
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
Highest resolution: 2.8 Å / Lowest resolution: 8 Å / Rfactor all: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.98

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