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- PDB-1gpo: CRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FA... -

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Basic information

Entry
Database: PDB / ID: 1gpo
TitleCRYSTAL STRUCTURE OF THE RATIONALLY DESIGNED ANTIBODY M41 AS A FAB FRAGMENT
Components(ANTIBODY M41) x 2
KeywordsIMMUNE SYSTEM / PROTEIN ENGINEERING / ANTIBODY DESIGN / IMMUNOGLOBULIN STRUCTURE / ANTIGEN-BINDING SITE / CANONICAL CONFORMATION / COMPLEMENTARITY-DETERMINING REGION
Function / homology
Function and homology information


phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / alpha-beta T cell receptor complex / IgG immunoglobulin complex / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response ...phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / alpha-beta T cell receptor complex / IgG immunoglobulin complex / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin mediated immune response / complement activation, classical pathway / antigen binding / B cell differentiation / positive regulation of phagocytosis / positive regulation of immune response / antibacterial humoral response / adaptive immune 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 / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant / Ig gamma-1 chain C region secreted form
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSchiweck, W. / Skerra, A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The rational construction of an antibody against cystatin: lessons from the crystal structure of an artificial Fab fragment.
Authors: Schiweck, W. / Skerra, A.
#1: Journal: Proteins / Year: 1995
Title: Fermenter Production of an Artificial Fab Fragment, Rationally Designed for the Antigen Cystatin, and its Optimized Crystallization Through Constant Domain Shuffling
Authors: Schiweck, W. / Skerra, A.
History
DepositionMar 27, 1997Processing site: BNL
Revision 1.0Apr 1, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 18, 2013Group: Source and taxonomy
Revision 1.4Apr 3, 2024Group: 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ANTIBODY M41
H: ANTIBODY M41
M: ANTIBODY M41
I: ANTIBODY M41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9036
Polymers96,7114
Non-polymers1922
Water11,692649
1
L: ANTIBODY M41
H: ANTIBODY M41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4513
Polymers48,3552
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-33 kcal/mol
Surface area19860 Å2
MethodPISA
2
M: ANTIBODY M41
I: ANTIBODY M41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4513
Polymers48,3552
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-35 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.470, 103.510, 113.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.997725, 0.020407, -0.064249), (-0.016606, -0.998111, -0.059147), (-0.065335, -0.057946, 0.996179)
Vector: 86.401, 111.177, 7.256)

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Components

#1: Antibody ANTIBODY M41


Mass: 24172.518 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PASK85-M41 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 W3110 / References: UniProt: P01837
#2: Antibody ANTIBODY M41


Mass: 24182.809 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PASK85-M41 / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 W3110 / References: EMBL: AJ303449, UniProt: P01868*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growpH: 6.5
Details: 2.0 M AMMONIUM SULFATE, 5 % DMSO, 0.1 M CACODYLATE PH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, sitting drop
Details: Schiweck, W., (1995) Proteins: Struct.,Funct., Genet., 23, 561.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulphate1reservoir
25 %(v/v)DMSO1reservoir
3100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 1, 1995
RadiationMonochromator: NICKEL FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→60 Å / Num. obs: 69136 / % possible obs: 84.6 % / Observed criterion σ(I): 0.5 / Redundancy: 2.6 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.95→2 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.215 / % possible all: 50.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HYBRID FAB FRAGMENT CONSISTING OF THE MODELLED STRUCTURE FOR THE ARTIFICIAL FV FRAGMENT M41 AND CONSTANT DOMAINS OF THE ANTI-LYSOZYME ANTIBODY HYHEL-10

Resolution: 1.95→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.283 -10 %
Rwork0.214 --
obs0.214 67792 81.3 %
Displacement parametersBiso mean: 28.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6622 0 10 649 7281
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.75
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.58
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 / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58

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