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- PDB-1t66: The structure of FAB with intermediate affinity for fluorescein. -

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Basic information

Entry
Database: PDB / ID: 1t66
TitleThe structure of FAB with intermediate affinity for fluorescein.
Components
  • immunoglobulin heavy chain
  • immunoglobulin light chain
KeywordsIMMUNE SYSTEM / Antibody / Fab / Fluorescein
Function / homology
Function and homology information


Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / : / Kappa light chain C_region / Ighg protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTerzyan, S. / Ramsland, P.A. / Voss Jr., E.W. / Herron, J.N. / Edmundson, A.B.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Three-dimensional Structures of Idiotypically Related Fabs with Intermediate and High Affinity for Fluorescein.
Authors: Terzyan, S. / Ramsland, P.A. / Voss Jr., E.W. / Herron, J.N. / Edmundson, A.B.
History
DepositionMay 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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
Remark 900SEQUENCE THE SEQUENCE REFERENCES ARE: E. A. KABAT, T. T. WU, M. REID-MILLER, H. M. PERRY, K. S. ...SEQUENCE THE SEQUENCE REFERENCES ARE: E. A. KABAT, T. T. WU, M. REID-MILLER, H. M. PERRY, K. S. GOTTESMAN, SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, U.S. PHS. W. D. BEDZYK, L. S. JOHNSON, G. S. RIORDAN, E. W. VOSS JR. (1989), COMPARISON OF VARIABLE REGION PRIMARY STRUCTURES WITHIN AN ANTI-FLUORESCINE IDIOTYPE FAMILY, J. BIOL. CHEM. V. 264, 1565-1569.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: immunoglobulin light chain
H: immunoglobulin heavy chain
C: immunoglobulin light chain
D: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0546
Polymers96,3904
Non-polymers6652
Water3,225179
1
L: immunoglobulin light chain
H: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5273
Polymers48,1952
Non-polymers3321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-24 kcal/mol
Surface area19850 Å2
MethodPISA
2
C: immunoglobulin light chain
D: immunoglobulin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5273
Polymers48,1952
Non-polymers3321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-25 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.640, 117.120, 154.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody immunoglobulin light chain /


Mass: 24167.814 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 9-40 murine-murine hybridoma / Organ: spleen / Variant: BALB/CV / Strain: BALB/C / References: GenBank: 18044164, UniProt: Q65ZC0*PLUS
#2: Antibody immunoglobulin heavy chain /


Mass: 24027.107 Da / Num. of mol.: 2 / Fragment: FAB / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: LYMPHOCYTE-PLASMA CELL / Cell line: 9-40 murine-murine hybridoma / Organ: spleen / Variant: BALB/CV / Strain: BALB/C / References: UniProt: Q91Z05*PLUS
#3: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN / Fluorescein


Mass: 332.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.7 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 286 K / pH: 6.2
Details: ammonium sulphate, sodium phosphate, pH 6.2, batch, temperature 286K, pH 6.20

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC MAXFLUX
RadiationMonochromator: OSMIC MAXFLUX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→47.1 Å / Num. obs: 49354 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 41.7 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.533 / Mean I/σ(I) obs: 1.8 / % possible all: 95.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLR

1flr


Resolution: 2.3→47 Å / Isotropic thermal model: ANISOTROPIC OVERALL B-FACTOR / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.253 2299 4.5 %RANDOM
Rwork0.204 ---
obs0.204 46008 91 %-
all-49354 --
Solvent computationSolvent model: CNSL / Bsol: 42.59 Å2 / ksol: 0.312 e/Å3
Displacement parametersBiso mean: 43.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.459 Å20 Å20 Å2
2--21.398 Å20 Å2
3----15.939 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6776 0 50 179 7005
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.77
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_it1.4171.5
X-RAY DIFFRACTIONc_mcangle_it2.4742
X-RAY DIFFRACTIONc_scbond_it1.8612
X-RAY DIFFRACTIONc_scangle_it2.8432.5

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