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- PDB-4dcq: Crystal Structure of the Fab Fragment of 3B5H10, an Antibody-Spec... -

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Basic information

Entry
Database: PDB / ID: 4dcq
TitleCrystal Structure of the Fab Fragment of 3B5H10, an Antibody-Specific for Extended Polyglutamine Repeats (orthorhombic form)
Components
  • 3B5H10 FAB Heavy Chain
  • 3B5H10 FAB Light Chain
KeywordsIMMUNE SYSTEM / Fab fragment / immunoglobulin domain / anti-polyglutamine / polyglutamine repeats
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsPeters-Libeu, C.A. / Tran, T. / Finkbeiner, S. / Weisgraber, K.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Disease-associated polyglutamine stretches in monomeric huntingtin adopt a compact structure.
Authors: Peters-Libeu, C. / Miller, J. / Rutenber, E. / Newhouse, Y. / Krishnan, P. / Cheung, K. / Hatters, D. / Brooks, E. / Widjaja, K. / Tran, T. / Mitra, S. / Arrasate, M. / Mosquera, L.A. / ...Authors: Peters-Libeu, C. / Miller, J. / Rutenber, E. / Newhouse, Y. / Krishnan, P. / Cheung, K. / Hatters, D. / Brooks, E. / Widjaja, K. / Tran, T. / Mitra, S. / Arrasate, M. / Mosquera, L.A. / Taylor, D. / Weisgraber, K.H. / Finkbeiner, S.
History
DepositionJan 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Sep 13, 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_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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3B5H10 FAB Light Chain
B: 3B5H10 FAB Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2234
Polymers47,0992
Non-polymers1242
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-26 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.068, 121.815, 42.012
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-476-

HOH

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Components

#1: Antibody 3B5H10 FAB Light Chain


Mass: 23611.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: monoclonal antibody / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA
#2: Antibody 3B5H10 FAB Heavy Chain


Mass: 23487.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: monoclonal antibody / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 3350, 200 mM citric acid,0.7% ethylene glycol, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→30 Å / Num. all: 32012 / Num. obs: 29497 / % possible obs: 96.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.071 / Net I/σ(I): 7.6
Reflection shellResolution: 1.94→1.99 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1525 / Rsym value: 0.27 / % possible all: 74.26

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.2 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å19.86 Å
Translation4 Å19.86 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALEPACKdata scaling
PHASER1.3.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S96

3s96


Resolution: 1.94→11 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.2418 / WRfactor Rwork: 0.184 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8356 / SU B: 4.089 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1994 / SU Rfree: 0.1801 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.199 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1461 5 %RANDOM
Rwork0.1852 ---
all0.1883 29209 --
obs0.1883 29209 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 73.13 Å2 / Biso mean: 25.4097 Å2 / Biso min: 8.44 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.37 Å20 Å2
3---1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.94→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3316 0 8 365 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223460
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.954730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2965450
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.41325.077130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1515549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.798156
X-RAY DIFFRACTIONr_chiral_restr0.1460.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212605
X-RAY DIFFRACTIONr_mcbond_it1.3011.52195
X-RAY DIFFRACTIONr_mcangle_it2.2423578
X-RAY DIFFRACTIONr_scbond_it3.23931265
X-RAY DIFFRACTIONr_scangle_it4.9174.51144
LS refinement shellResolution: 1.94→1.989 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 76 -
Rwork0.218 1525 -
all-1601 -
obs-1525 74.26 %

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