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- PDB-3d8f: Crystal structure of the human Fe65-PTB1 domain with bound phosph... -

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Basic information

Entry
Database: PDB / ID: 3d8f
TitleCrystal structure of the human Fe65-PTB1 domain with bound phosphate (trigonal crystal form)
ComponentsAmyloid beta A4 precursor protein-binding family B member 1
KeywordsPROTEIN BINDING / alpha-beta structure / phosphotyrosine binding domain
Function / homology
Function and homology information


negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / amyloid-beta binding ...negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / amyloid-beta binding / chromatin organization / histone binding / growth cone / transcription coactivator activity / molecular adaptor activity / nuclear speck / positive regulation of apoptotic process / synapse / apoptotic process / DNA damage response / chromatin binding / ubiquitin protein ligase binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / 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
PHOSPHATE ION / Amyloid beta precursor protein binding family B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsRadzimanowski, J. / Ravaud, S. / Sinning, I. / Wild, K.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of the human Fe65-PTB1 domain.
Authors: Radzimanowski, J. / Ravaud, S. / Schlesinger, S. / Koch, J. / Beyreuther, K. / Sinning, I. / Wild, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Mercury-induced crystallization and SAD phasing of the human Fe65-PTB1 domain.
Authors: Radzimanowski, J. / Ravaud, S. / Beyreuther, K. / Sinning, I. / Wild, K.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Amyloid beta A4 precursor protein-binding family B member 1
B: Amyloid beta A4 precursor protein-binding family B member 1
C: Amyloid beta A4 precursor protein-binding family B member 1
D: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3196
Polymers67,1294
Non-polymers1902
Water39622
1
A: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8772
Polymers16,7821
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amyloid beta A4 precursor protein-binding family B member 1


Theoretical massNumber of molelcules
Total (without water)16,7821
Polymers16,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8772
Polymers16,7821
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amyloid beta A4 precursor protein-binding family B member 1


Theoretical massNumber of molelcules
Total (without water)16,7821
Polymers16,7821
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.040, 146.040, 78.294
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Amyloid beta A4 precursor protein-binding family B member 1 / Fe65-PTB1 / Fe65 protein


Mass: 16782.211 Da / Num. of mol.: 4 / Fragment: Phosphotyrosine binding domain 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65, RIR / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O00213
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES, 5% (v/v) ethylene glycol, 50mM Na2HPO4, 10% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 19, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 17113 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.9
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.7→49.21 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.888 / SU B: 16.656 / SU ML: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.74 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.313 865 5.1 %RANDOM
Rwork0.242 ---
obs0.245 17104 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.18 Å20 Å2
2---0.36 Å20 Å2
3---0.54 Å2
Refine analyzeLuzzati sigma a obs: 0.404 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 10 22 4000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224036
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.9685437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.14624.022179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.52815755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6971532
X-RAY DIFFRACTIONr_chiral_restr0.0920.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022946
X-RAY DIFFRACTIONr_nbd_refined0.2510.21864
X-RAY DIFFRACTIONr_nbtor_refined0.3160.22717
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3580.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.24
X-RAY DIFFRACTIONr_mcbond_it0.9421.52570
X-RAY DIFFRACTIONr_mcangle_it1.63224016
X-RAY DIFFRACTIONr_scbond_it1.91831639
X-RAY DIFFRACTIONr_scangle_it3.3334.51421
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 64 -
Rwork0.33 1215 -
all-1279 -
obs--100 %

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