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- PDB-1fl3: CRYSTAL STRUCTURE OF THE BLUE FLUORESCENT ANTIBODY (19G2) IN COMP... -

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Basic information

Entry
Database: PDB / ID: 1fl3
TitleCRYSTAL STRUCTURE OF THE BLUE FLUORESCENT ANTIBODY (19G2) IN COMPLEX WITH STILBENE HAPTEN AT 277K
Components
  • BLUE FLUORESCENT ANTIBODY (19G2)-HEAVY CHAIN
  • BLUE FLUORESCENT ANTIBODY (19G2)-LIGHT CHAIN
KeywordsIMMUNE SYSTEM / immunoglobulin fold
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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / 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 / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / phagocytosis, engulfment / immunoglobulin complex, circulating / immunoglobulin receptor binding / immunoglobulin mediated immune response / complement activation, classical pathway / positive regulation of phagocytosis / antigen binding / B cell differentiation / positive regulation of immune response / antibacterial humoral response / extracellular space / extracellular region / plasma membrane
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/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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsStevens, R.C. / Beuscher IV, A.E.
CitationJournal: Science / Year: 2000
Title: Blue-fluorescent antibodies.
Authors: Simeonov, A. / Matsushita, M. / Juban, E.A. / Thompson, E.H. / Hoffman, T.Z. / Beuscher IV, A.E. / Taylor, M.J. / Wirsching, P. / Rettig, W. / McCusker, J.K. / Stevens, R.C. / Millar, D.P. / ...Authors: Simeonov, A. / Matsushita, M. / Juban, E.A. / Thompson, E.H. / Hoffman, T.Z. / Beuscher IV, A.E. / Taylor, M.J. / Wirsching, P. / Rettig, W. / McCusker, J.K. / Stevens, R.C. / Millar, D.P. / Schultz, P.G. / Lerner, R.A. / Janda, K.D.
History
DepositionAug 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Category: reflns / Item: _reflns.percent_possible_obs
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: BLUE FLUORESCENT ANTIBODY (19G2)-HEAVY CHAIN
L: BLUE FLUORESCENT ANTIBODY (19G2)-LIGHT CHAIN
A: BLUE FLUORESCENT ANTIBODY (19G2)-HEAVY CHAIN
B: BLUE FLUORESCENT ANTIBODY (19G2)-LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,1826
Polymers90,5634
Non-polymers6192
Water4,017223
1
H: BLUE FLUORESCENT ANTIBODY (19G2)-HEAVY CHAIN
L: BLUE FLUORESCENT ANTIBODY (19G2)-LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5913
Polymers45,2822
Non-polymers3091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-20 kcal/mol
Surface area18990 Å2
MethodPISA
2
A: BLUE FLUORESCENT ANTIBODY (19G2)-HEAVY CHAIN
B: BLUE FLUORESCENT ANTIBODY (19G2)-LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5913
Polymers45,2822
Non-polymers3091
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-20 kcal/mol
Surface area19230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.930, 62.069, 93.539
Angle α, β, γ (deg.)90.00, 117.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody BLUE FLUORESCENT ANTIBODY (19G2)-HEAVY CHAIN


Mass: 21957.736 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01867*PLUS
#2: Antibody BLUE FLUORESCENT ANTIBODY (19G2)-LIGHT CHAIN


Mass: 23323.854 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) 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


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.8 Å3/Da / Density % sol: 56.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG4000, magnesium chloride, sodium citrate, methionine, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Mar 31, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.42→99 Å / Num. all: 36035 / Num. obs: 36035 / Observed criterion σ(F): -2 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29
Reflection shellResolution: 2.42→2.51 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.295 / Num. unique all: 2648 / % possible all: 70

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
RefinementResolution: 2.45→20 Å / σ(F): 0 / σ(I): 0
Stereochemistry target values: maximum likelihood target using amplitudes
RfactorNum. reflection% reflectionSelection details
Rfree0.262 999 -RANDOM
Rwork0.231 ---
all0.1 33250 --
obs0.1 33250 95.2 %-
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6364 0 46 223 6633

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