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- PDB-1ivl: THE DE NOVO DESIGN OF AN ANTIBODY COMBINING SITE: CRYSTALLOGRAPHI... -

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Basic information

Entry
Database: PDB / ID: 1ivl
TitleTHE DE NOVO DESIGN OF AN ANTIBODY COMBINING SITE: CRYSTALLOGRAPHIC ANALYSIS OF THE VL DOMAIN CONFIRMS THE STRUCTURAL MODEL
ComponentsIGG-KAPPA M29B FV (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ISOPROPYL ALCOHOL / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.17 Å
AuthorsEssen, L.-O. / Skerra, A.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: The de novo design of an antibody combining site. Crystallographic analysis of the VL domain confirms the structural model.
Authors: Essen, L.O. / Skerra, A.
#1: Journal: J.Chromatogr.,A / Year: 1993
Title: Single-Step Purification of a Bacterially Expressed Antibody FV Fragment by Immobilized Metal Affinity Chromatography in the Presence of Betaine
Authors: Essen, L.-O. / Skerra, A.
History
DepositionMay 4, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG-KAPPA M29B FV (LIGHT CHAIN)
B: IGG-KAPPA M29B FV (LIGHT CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3903
Polymers23,3302
Non-polymers601
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.890, 58.050, 83.220
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 A 8 / 2: CIS PROLINE - PRO A 95 / 3: CIS PROLINE - PRO B 8 / 4: CIS PROLINE - PRO B 95 / 5: RESIDUES ARG A 24 AND B 24 ARE PARTIALLY DISORDERED.

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Components

#1: Antibody IGG-KAPPA M29B FV (LIGHT CHAIN)


Mass: 11664.921 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 196585
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE PRESENTED IN THIS ENTRY IS DESCRIBED IN THE JRNL ARTICLE LISTED ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.31 %
Crystal grow
*PLUS
Temperature: 16-22 ℃ / pH: 5.75 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlprotein1drop
220 %(v/v)isopropanol1reservoir
320 %(w/v)PEG40001reservoir
40.1 Msodium citrate1reservoir
50.1 mMEDTA1reservoir
60.01 %(w/v)sodium azide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.17 Å / Lowest resolution: 20 Å / Num. obs: 12009 / % possible obs: 91 % / Observed criterion σ(I): 2 / Num. measured all: 69140 / Rmerge(I) obs: 0.06

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.17→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.175 -
obs0.175 11378
Refinement stepCycle: LAST / Resolution: 2.17→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1644 0 4 85 1733
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.7
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
Rfactor obs: 0.175
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 19.71 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d1.7
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_improper_angle_d2.4

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