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- PDB-1fig: ROUTES TO CATALYSIS: STRUCTURE OF A CATALYTIC ANTIBODY AND COMPAR... -

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Basic information

Entry
Database: PDB / ID: 1fig
TitleROUTES TO CATALYSIS: STRUCTURE OF A CATALYTIC ANTIBODY AND COMPARISON WITH ITS NATURAL COUNTERPART
Components
  • IGG1-KAPPA 1F7 FAB (HEAVY CHAIN)
  • IGG1-KAPPA 1F7 FAB (LIGHT CHAIN)
KeywordsIMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-TSA / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsHaynes, M.R. / Stura, E.A. / Hilvert, D. / Wilson, I.A.
CitationJournal: Science / Year: 1994
Title: Routes to catalysis: structure of a catalytic antibody and comparison with its natural counterpart.
Authors: Haynes, M.R. / Stura, E.A. / Hilvert, D. / Wilson, I.A.
History
DepositionJan 7, 1994Processing site: BNL
Revision 1.0May 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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
L: IGG1-KAPPA 1F7 FAB (LIGHT CHAIN)
H: IGG1-KAPPA 1F7 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7063
Polymers46,4782
Non-polymers2281
Water181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3500 Å2
ΔGint-25 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.100, 63.300, 178.500
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
2: VAL L 58 - PRO L 59 OMEGA =149.81 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
3: CIS PROLINE - PRO L 95
4: PRO L 119 - PRO L 120 OMEGA =216.92 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
5: CIS PROLINE - PRO L 141 / 6: CIS PROLINE - PRO H 9
7: SER H 75 - SER H 76 OMEGA =145.05 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION
8: CIS PROLINE - PRO H 149 / 9: CIS PROLINE - PRO H 151 / 10: CIS PROLINE - PRO H 200
11: TSA IS THE TRANSITION STATE ANALOG HAPTEN USED TO ELICIT 1F7.

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Components

#1: Antibody IGG1-KAPPA 1F7 FAB (LIGHT CHAIN)


Mass: 23302.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 196805
#2: Antibody IGG1-KAPPA 1F7 FAB (HEAVY CHAIN)


Mass: 23174.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 194362
#3: Chemical ChemComp-TSA / 8-HYDROXY-2-OXA-BICYCLO[3.3.1]NON-6-ENE-3,5-DICARBOXYLIC ACID


Mass: 228.199 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTSA IS THE TRANSITION STATE ANALOG HAPTEN USED TO ELICIT 1F7.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal grow
*PLUS
Temperature: 22.5 ℃ / pH: 7.25 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.62 Mammonium sulfate1reservoir
20.06 MPIPES1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 8660 / % possible obs: 95.8 % / Num. measured all: 19033 / Rmerge(I) obs: 0.086

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→12 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.22 -
obs0.22 19033
Refinement stepCycle: LAST / Resolution: 3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3267 0 16 1 3284
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg4.06
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2
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
Num. reflection all: 19033 / Rfactor all: 0.22 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d4.06
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg2

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