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- PDB-2dyq: Crystal Structure of the C-terminal Phophotyrosine Interaction Do... -

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Basic information

Entry
Database: PDB / ID: 2dyq
TitleCrystal Structure of the C-terminal Phophotyrosine Interaction Domain of Human APBB3
ComponentsAmyloid beta A4 precursor protein-binding family B member 3
KeywordsPROTEIN BINDING / Phosphotyrosine-interaction domain (PTB/PID) / Alzheimer's disease / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


low-density lipoprotein particle receptor binding / positive regulation of protein secretion / actin cytoskeleton / amyloid-beta binding / nuclear body / regulation of DNA-templated transcription / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Amyloid beta precursor protein binding family B member 1/2/3 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...Amyloid beta precursor protein binding family B member 1/2/3 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta A4 precursor protein-binding family B member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsNishino, A. / Saijo, S. / Kishishita, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of the C-terminal Phophotyrosine Interaction Domain of Human APBB3
Authors: Saijo, S. / Nishino, A. / Kishishita, S. / Shirouzu, M. / Yokoyama, S.
History
DepositionSep 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid beta A4 precursor protein-binding family B member 3


Theoretical massNumber of molelcules
Total (without water)15,5851
Polymers15,5851
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.292, 82.292, 104.871
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Amyloid beta A4 precursor protein-binding family B member 3 / Fe65-like protein 2 / Fe65L2


Mass: 15584.754 Da / Num. of mol.: 1
Fragment: C-terminal Phosphotyrosine interaction domain (PTB/PID)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: APBB3, FE65L2 / Plasmid: PK060110-10 / References: UniProt: O95704

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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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 25% PEG 3350, 0.2M Ammonium Acetate, 0.1M Tris-HCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.97895 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 19, 2006 / Details: mirrors
RadiationMonochromator: Fixed exit Si double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 3.1→71.25 Å / Num. obs: 4171 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 18.4 % / Biso Wilson estimate: 45.2 Å2 / Rsym value: 0.08 / Net I/σ(I): 51.3
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 8.6 / Num. unique all: 202 / Rsym value: 0.407 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.852 / SU B: 50.292 / SU ML: 0.387 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.37 / ESU R Free: 0.452 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.298 190 4.6 %RANDOM
Rwork0.254 ---
obs0.256 3946 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å2-0.19 Å20 Å2
2---0.37 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 0 0 0 909
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5931.9451272
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5255122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.6232534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.2815132
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.341152
X-RAY DIFFRACTIONr_chiral_restr0.1090.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02706
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.2433
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2661
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.221
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3760.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5651.5629
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8962979
X-RAY DIFFRACTIONr_scbond_it1.373349
X-RAY DIFFRACTIONr_scangle_it2.1374.5293
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.105→3.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 7 -
Rwork0.289 281 -
obs-281 100 %
Refinement TLS params.Method: refined / Origin x: 32.012 Å / Origin y: 36.536 Å / Origin z: 11.352 Å
111213212223313233
T0.3211 Å2-0.0185 Å20.1146 Å2-0.302 Å2-0.0946 Å2--0.087 Å2
L14.5348 °2-2.5729 °22.9767 °2-4.1423 °2-1.5259 °2--4.1592 °2
S0.3498 Å °0.9209 Å °0.2079 Å °0.2345 Å °0.1052 Å °0.1194 Å °-0.0761 Å °0.286 Å °-0.455 Å °

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