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- PDB-1seq: Fab MNAC13 -

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Basic information

Entry
Database: PDB / ID: 1seq
TitleFab MNAC13
Components(Monoclonal Antibody ...) x 2
KeywordsIMMUNE SYSTEM / Immunoglobulin
Function / homology
Function and homology information


humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding ...humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin mediated immune response / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / defense response to bacterium / external side of plasma membrane / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsCovaceuszach, S. / Cattaneo, A. / Lamba, D.
Citation
Journal: Proteins / Year: 2005
Title: Neutralization of NGF-TrkA Receptor Interaction by the Novel Antagonistic anti-TrkA Monoclonal Antibody MNAC13: a Structural Insight
Authors: Covaceuszach, S. / Cattaneo, A. / Lamba, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Purification, crystallization and preliminary X-ray analysis of the Fab fragment from MNAC13, a novel antagonistic anti-tyrosine kinase A receptor monoclonal antibody
Authors: Covaceuszach, S. / Cattaneo, A. / Lamba, D.
History
DepositionFeb 18, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of this protein is not available in any of the database sequence. Author ...SEQUENCE The sequence of this protein is not available in any of the database sequence. Author states that Glu:L17; Glu:L18; Glu:L81; Asp:L142 are considered as Ser due to decarboxylation (radiation damage).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Monoclonal Antibody MNAC13
H: Monoclonal Antibody MNAC13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7048
Polymers47,1372
Non-polymers5666
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-65 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.731, 67.546, 111.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody Monoclonal Antibody MNAC13


Mass: 23107.381 Da / Num. of mol.: 1 / Fragment: FAB Light Chain / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#2: Antibody Monoclonal Antibody MNAC13


Mass: 24030.076 Da / Num. of mol.: 1 / Fragment: FAB Heavy Chain / Source method: isolated from a natural source / Details: Hybridoma / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01868*PLUS

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Non-polymers , 4 types, 357 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.17 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2 M ammonium sulfate, 5%(v/v) 2-propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 18, 2000 / Details: Sagitally focusing Ge(220) and a multilayer
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.78→39 Å / Num. obs: 38392 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.063 / Net I/σ(I): 8.2
Reflection shellResolution: 1.78→1.83 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.1 / Num. unique all: 1893 / Rsym value: 0.398 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BM3

1bm3


Resolution: 1.78→38.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1775680.62 / Data cutoff high rms absF: 1775680.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3836 10 %RANDOM
Rwork0.194 ---
all0.194 38392 --
obs0.194 38350 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.8362 Å2 / ksol: 0.358609 e/Å3
Displacement parametersBiso mean: 24.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å20 Å2
2--3.59 Å20 Å2
3----1.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.78→38.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3238 0 28 355 3621
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 1.78→1.89 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.27 644 11 %
Rwork0.247 5224 -
obs-1893 91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3SO4.PARAM
X-RAY DIFFRACTION4TRIS.PARAM
X-RAY DIFFRACTION5ALC.PARAM

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