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- PDB-3ln9: Crystal structure of the fibril-specific B10 antibody fragment -

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Basic information

Entry
Database: PDB / ID: 3ln9
TitleCrystal structure of the fibril-specific B10 antibody fragment
ComponentsImmunoglobulin heavy chain antibody variable domain B10
KeywordsIMMUNE SYSTEM / Complementarity Determining Regions / CDR / Camelids / Immunoglobulin Heavy Chains / fibril-specific / fibril recognition / Alzheimer's disease / Amyloid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRATE ANION
Function and homology information
Biological speciesCamelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsParthier, C. / Morgado, I. / Stubbs, M.T. / Faendrich, M.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Amyloid Fibril Recognition with the Conformational B10 Antibody Fragment Depends on Electrostatic Interactions.
Authors: Haupt, C. / Morgado, I. / Kumar, S.T. / Parthier, C. / Bereza, M. / Hortschansky, P. / Stubbs, M.T. / Horn, U. / Fandrich, M.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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

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Assembly

Deposited unit
A: Immunoglobulin heavy chain antibody variable domain B10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3126
Polymers15,7501
Non-polymers5615
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.124, 84.124, 84.124
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23
Components on special symmetry positions
IDModelComponents
11A-140-

SO4

21A-184-

HOH

31A-255-

HOH

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Components

#1: Antibody Immunoglobulin heavy chain antibody variable domain B10


Mass: 15750.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Protein was selected by phage display from a fully synthetic library that was partly based on naturally occurring sequences from Camelidae
Source: (gene. exp.) Camelidae (mammal) / Plasmid: p416His / Production host: Escherichia coli (E. coli) / Strain (production host): TG-1
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUES (-3)-0 ASP TYR LYS ASP ARE N-TERMINAL FLAG TAGS AND RESIDUES HIS 130-135 ARE C-TERMINAL HIS TAGS.

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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: 3.15 Å3/Da / Density % sol: 60.95 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 200mM Sodium Citrate, 2M Ammonium Sulphate, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 5, 2009
RadiationMonochromator: Double crystal monochromator with 2 sets of mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 19869 / Num. obs: 19838 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 5.5 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.063 / Net I/σ(I): 21.05
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.624 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2955 / Rsym value: 0.69 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.4.0062refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OL0

1ol0


Resolution: 1.8→18.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.935 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.106 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23295 932 5 %RANDOM
Rwork0.19696 ---
all0.19876 17722 --
obs0.19876 17722 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.991 Å2
Refinement stepCycle: LAST / Resolution: 1.8→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms984 0 36 116 1136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9181.9481414
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2135125
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69122.24549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.22115164
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2891510
X-RAY DIFFRACTIONr_chiral_restr0.1050.2143
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021802
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9811.5619
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6162996
X-RAY DIFFRACTIONr_scbond_it2.6693428
X-RAY DIFFRACTIONr_scangle_it3.9154.5418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 66 -
Rwork0.29 1260 -
obs-1260 100 %
Refinement TLS params.Method: refined / Origin x: 11.287 Å / Origin y: -27.963 Å / Origin z: 3.668 Å
111213212223313233
T-0.0512 Å2-0.0381 Å20.1232 Å2--0.2856 Å2-0.0425 Å2---0.1742 Å2
L2.3275 °2-1.9356 °20.5305 °2-5.4416 °2-0.6516 °2--1.7654 °2
S0.2146 Å °-0.2079 Å °0.3136 Å °-0.7148 Å °0.0087 Å °-0.7145 Å °0.1479 Å °-0.0223 Å °-0.2233 Å °

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