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- PDB-1ub5: Crystal structure of Antibody 19G2 with hapten at 100K -

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Basic information

Entry
Database: PDB / ID: 1ub5
TitleCrystal structure of Antibody 19G2 with hapten at 100K
Components
  • antibody 19G2, alpha chain
  • antibody 19G2, beta chain
KeywordsIMMUNE SYSTEM / antibody fluorscence dynamics / sera ligand
Function / homology
Function and homology information


Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity ...Initial triggering of complement / Classical antibody-mediated complement activation / FCGR activation / Role of phospholipids in phagocytosis / Regulation of Complement cascade / Regulation of actin dynamics for phagocytic cup formation / humoral immune response mediated by circulating immunoglobulin / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / Fc-gamma receptor I complex binding / phagocytosis, engulfment / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / 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 / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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 V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / 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
4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID / Immunoglobulin kappa constant / Immunoglobulin heavy constant gamma 2B / Ig heavy chain V region 914
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBeuscher, A.B. / Wirsching, P. / Lerner, R.A. / Janda, K. / Stevens, R.C.
CitationJournal: To be published
Title: Structure and Dynamics of Blue Fluorescent Antibody 19G2 at Blue and Violet Fluorescent Temperatures
Authors: Beuscher, A.B. / Wirsching, P. / Lerner, R.A. / Janda, K. / Stevens, R.C.
History
DepositionMar 30, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: antibody 19G2, alpha chain
L: antibody 19G2, beta chain
A: antibody 19G2, alpha chain
B: antibody 19G2, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,9176
Polymers91,2984
Non-polymers6192
Water10,034557
1
H: antibody 19G2, alpha chain
L: antibody 19G2, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9593
Polymers45,6492
Non-polymers3091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-20 kcal/mol
Surface area19010 Å2
MethodPISA
2
A: antibody 19G2, alpha chain
B: antibody 19G2, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9593
Polymers45,6492
Non-polymers3091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-20 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.933, 61.058, 92.589
Angle α, β, γ (deg.)90.00, 117.05, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein antibody 19G2, alpha chain


Mass: 22215.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse) / References: UniProt: P18527, UniProt: P01867*PLUS
#2: Protein antibody 19G2, beta chain


Mass: 23434.055 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell (production host): hybridoma cell / Production host: Mus musculus (house mouse) / References: UniProt: P01837*PLUS
#3: Chemical ChemComp-SPB / 4-(4-STYRYL-PHENYLCARBAMOYL)-BUTYRIC ACID / 5-OXO-5-({4-[(E)-2-PHENYLVINYL]PHENYL}AMINO)PENTANOIC ACID / N-(TRANS-4-STILBENYL)-5-AMINO-5-OXO-PENTANOIC ACID


Mass: 309.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.51 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG2000, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→19.89 Å / Num. all: 76903 / Observed criterion σ(F): 0 / Biso Wilson estimate: 17.6 Å2 / Limit h max: 92 / Limit h min: -103 / Limit k max: 32 / Limit k min: -103 / Limit l max: 48 / Limit l min: 0 / Observed criterion F max: 211600.69 / Observed criterion F min: 0.32

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→19.89 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3207 5 %random
Rwork0.248 ---
all-66117 --
obs-63535 96.1 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.4994 Å2 / ksol: 0.359855 e/Å3
Displacement parametersBiso max: 105.27 Å2 / Biso mean: 44.8 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å20 Å2-0.04 Å2
2---0.62 Å20 Å2
3---1.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6414 0 46 557 7017
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d26.2
X-RAY DIFFRACTIONc_improper_angle_d0.75
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.294064.90.29172200.0148255762692.4
2.09-2.20.2723904.80.27273010.0148208769193.7
2.2-2.340.3063614.40.30671690.0168236753091.4
2.34-2.520.2753844.70.27575820.0148241796696.7
2.52-2.770.2574074.90.25876520.0138250805997.7
2.77-3.170.274415.30.26977080.0138259814998.7
3.17-3.990.24641650.24578000.0128303821699
3.99-19.890.2064024.80.20778960.018447829898.2
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3fra.paramfra.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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