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- PDB-4amk: Fab fragment of antiporphrin antibody 13g10 -

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Basic information

Entry
Database: PDB / ID: 4amk
TitleFab fragment of antiporphrin antibody 13g10
Components
  • FAB13G10, HEAVY CHAIN
  • FAB13G10, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / 13G10 / METALLOPORPHYRIN / CATALYTIC ANTIBODY / PEROXIDASE
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsMahy, J.P. / Golinelli-Pimpaneau, B.
Citation
Journal: Plos One / Year: 2012
Title: Crystal Structure of Two Anti-Porphyrin Antibodies with Peroxidase Activity.
Authors: Munoz Robles, V. / Marechal, J. / Bahloul, A. / Sari, M. / Mahy, J. / Golinelli-Pimpaneau, B.
#1: Journal: FEBS Lett. / Year: 1996
Title: Artificial Peroxidase-Like Hemoproteins Based on Antibodies Constructed from a Specifically Designed Ortho-Carboxy Substituted Tetraarylporphyrin Hapten and Exhibiting a High Affinity for Iron-Porphyrins.
Authors: Quilez, R. / De Lauzon, S. / Desfosses, B. / Mansuy, D. / Mahy, J.P.
#2: Journal: FEBS Lett. / Year: 1999
Title: Studies of the Reactivity of Artificial Peroxidase-Like Hemoproteins Based on Antibodies Elicited Against a Specifically Designed Ortho-Carboxy Substituted Tetraarylporphyrin.
Authors: De Lauzon, S. / Desfosses, B. / Mansuy, D. / Mahy, J.P.
History
DepositionMar 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Mar 4, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FAB13G10, HEAVY CHAIN
L: FAB13G10, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9306
Polymers45,6292
Non-polymers3014
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-29.9 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.800, 62.750, 113.500
Angle α, β, γ (deg.)90.00, 91.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody FAB13G10, HEAVY CHAIN


Mass: 22877.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA
#2: Antibody FAB13G10, LIGHT CHAIN


Mass: 22751.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MURINE HYBRIDOMA
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.99 Å3/Da / Density % sol: 38 % / Description: NONE
Crystal growpH: 8.5
Details: 26.5 % PEG 2000, 0.2 M MGCL2, 0.1 M TRIS PH 8.5, 10% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 8, 2001
RadiationMonochromator: 0.97 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→25 Å / Num. obs: 23580 / % possible obs: 93.7 % / Redundancy: 2.5 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.7
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 4.6 / % possible all: 91.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MFA AND 1MFE

1mfa

1mfe


Resolution: 2.05→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE SIDE CHAINS OF SER L32, SER L95 AND GLN H196, WHICH WERE NOT OBSERVED IN THE ELECTRON DENSITY, WERE MODELLED AS ALANINES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2751 1116 4.5 %RANDOM
Rwork0.2244 ---
obs0.2244 23227 93.9 %-
Solvent computationBsol: 69.7339 Å2 / ksol: 0.397451 e/Å3
Displacement parametersBiso mean: 49 Å2
Baniso -1Baniso -2Baniso -3
1-5.846 Å20 Å2-1.798 Å2
2---9.308 Å20 Å2
3---3.462 Å2
Refinement stepCycle: LAST / Resolution: 2.05→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 19 188 3377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007712
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.52199
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.05→2.08 Å / Total num. of bins used: 22 /
RfactorNum. reflection
Rfree0.451 57
Rwork0.339 986
Xplor fileSerial no: 1 / Param file: GOL.PAR / Topol file: GOL.TOP

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