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- PDB-5dyo: Fab43.1 complex with flourescein -

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Basic information

Entry
Database: PDB / ID: 5dyo
TitleFab43.1 complex with flourescein
Components
  • Fab 43.1 Heavy Chain
  • Fab 43.1 Light Chain
KeywordsIMMUNE SYSTEM / antibody Fab Flourescein
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsLongenecker, K.L. / Judge, R.A.
CitationJournal: Biopolymers / Year: 2016
Title: Three-dimensional structure, binding, and spectroscopic characteristics of the monoclonal antibody 43.1 directed to the carboxyphenyl moiety of fluorescein.
Authors: Gayda, S. / Longenecker, K.L. / Judge, R.A. / Swift, K.M. / Manoj, S. / Linthicum, D.S. / Tetin, S.Y.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 2.0Sep 20, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / pdbx_struct_oper_list / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _pdbx_struct_oper_list.symmetry_operation / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Mar 21, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.pdbx_collection_date
Revision 2.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab 43.1 Heavy Chain
B: Fab 43.1 Light Chain
H: Fab 43.1 Heavy Chain
L: Fab 43.1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,66311
Polymers93,5184
Non-polymers1,1457
Water6,702372
1
A: Fab 43.1 Heavy Chain
B: Fab 43.1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2835
Polymers46,7592
Non-polymers5243
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-34 kcal/mol
Surface area19390 Å2
MethodPISA
2
H: Fab 43.1 Heavy Chain
L: Fab 43.1 Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3796
Polymers46,7592
Non-polymers6204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-62 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.232, 105.401, 109.059
Angle α, β, γ (deg.)90.000, 102.730, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Fab 43.1 Heavy Chain


Mass: 22643.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Fab 43.1 Light Chain


Mass: 24115.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Chemical ChemComp-FLU / 2-(6-HYDROXY-3-OXO-3H-XANTHEN-9-YL)-BENZOIC ACID / FLUORESCEIN


Mass: 332.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H12O5
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 3.25 Å3/Da / Density % sol: 62.17 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 4.6 / Details: ammonium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97971 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97971 Å / Relative weight: 1
ReflectionResolution: 2.36→47.2 Å / Num. obs: 49365 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 10
Reflection shellResolution: 2.357→2.365 Å / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.6refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OCX

4ocx


Resolution: 2.36→47.2 Å / Cor.coef. Fo:Fc: 0.9116 / Cor.coef. Fo:Fc free: 0.8818 / SU R Cruickshank DPI: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.26 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2457 5 %RANDOM
Rwork0.1933 ---
obs0.1955 49167 99.86 %-
Displacement parametersBiso max: 153.72 Å2 / Biso mean: 49.11 Å2 / Biso min: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1--9.9797 Å20 Å2-12.6309 Å2
2--11.9037 Å20 Å2
3----1.924 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å
Refinement stepCycle: final / Resolution: 2.36→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6508 0 75 372 6955
Biso mean--44.52 47.39 -
Num. residues----851
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2199SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes137HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1033HARMONIC5
X-RAY DIFFRACTIONt_it6749HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion907SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7462SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6749HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9209HARMONIC21.2
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion19.4
LS refinement shellResolution: 2.36→2.42 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2887 177 4.89 %
Rwork0.2341 3443 -
all0.2369 3620 -
obs--99.92 %

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