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- PDB-3s96: Crystal structure of 3B5H10 -

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Basic information

Entry
Database: PDB / ID: 3s96
TitleCrystal structure of 3B5H10
Components
  • 3B5H10 FAB heavy chain
  • 3B5H10 FAB light chain
KeywordsIMMUNE SYSTEM / FAB / huntingtin
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWeisgraber, K. / Peters-Libeu, C. / Rutenber, E. / Newhouse, Y. / Finkbeiner, S.
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
DepositionMay 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2012Group: Database references
Revision 1.2Apr 3, 2024Group: 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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3B5H10 FAB heavy chain
B: 3B5H10 FAB light chain
C: 3B5H10 FAB heavy chain
D: 3B5H10 FAB light chain


Theoretical massNumber of molelcules
Total (without water)94,6704
Polymers94,6704
Non-polymers00
Water16,033890
1
A: 3B5H10 FAB heavy chain
B: 3B5H10 FAB light chain


Theoretical massNumber of molelcules
Total (without water)47,3352
Polymers47,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-26 kcal/mol
Surface area20750 Å2
MethodPISA
2
C: 3B5H10 FAB heavy chain
D: 3B5H10 FAB light chain


Theoretical massNumber of molelcules
Total (without water)47,3352
Polymers47,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-25 kcal/mol
Surface area21000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.260, 78.250, 123.620
Angle α, β, γ (deg.)90.00, 90.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 3B5H10 FAB heavy chain


Mass: 23776.730 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA
#2: Antibody 3B5H10 FAB light chain


Mass: 23558.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: HYBRIDOMA
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.06 Å3/Da / Density % sol: 40 %
Crystal growpH: 4.5
Details: 7% PEG 3350, 66MM CITRIC ACID, 2 MM TRIS, 5% V/V ETHYL ACETATE, PH 4.50, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 323K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.078
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 70733 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rsym value: 0.081 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.236 / % possible all: 79

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0005refinement
MOSFLMdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A STRUCTURE DETERMINED FROM A SINGLE PT DERIVATIVE IN ANOTHER SPACE GROUP WAS USED AS THE PROBE MODEL FOR MOLECULAR REPLACEMENT.

Resolution: 1.9→11 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.874 / SU B: 4.103 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2826 5.1 %RANDOM
Rwork0.183 ---
obs0.187 52715 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: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20.26 Å2
2--0.21 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.9→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6420 0 0 890 7310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226597
X-RAY DIFFRACTIONr_bond_other_d0.1320.021
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9479001
X-RAY DIFFRACTIONr_angle_other_deg3.55632
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9095835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.29324.939245
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.753151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6031510
X-RAY DIFFRACTIONr_chiral_restr0.1340.21018
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024941
X-RAY DIFFRACTIONr_gen_planes_other0.0340.021
X-RAY DIFFRACTIONr_nbd_refined0.2280.22639
X-RAY DIFFRACTIONr_nbd_other0.4950.23
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24379
X-RAY DIFFRACTIONr_nbtor_other0.2330.22
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.2732
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.2147
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.267
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1821.54305
X-RAY DIFFRACTIONr_mcbond_other0.0751.51
X-RAY DIFFRACTIONr_mcangle_it1.92226813
X-RAY DIFFRACTIONr_scbond_it2.84332689
X-RAY DIFFRACTIONr_scangle_it4.0984.52188
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 99 -
Rwork0.189 2015 -
obs--100 %

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