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- PDB-3suz: Crystal structure of Rat Mint2 PPC -

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Basic information

Entry
Database: PDB / ID: 3suz
TitleCrystal structure of Rat Mint2 PPC
ComponentsAmyloid beta A4 precursor protein-binding family A member 2
KeywordsPROTEIN BINDING / APP binding
Function / homology
Function and homology information


synaptic vesicle exocytosis / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / locomotory behavior / Schaffer collateral - CA1 synapse / multicellular organism growth / protein transport / presynapse / amyloid-beta binding / regulation of gene expression ...synaptic vesicle exocytosis / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / locomotory behavior / Schaffer collateral - CA1 synapse / multicellular organism growth / protein transport / presynapse / amyloid-beta binding / regulation of gene expression / chemical synaptic transmission / in utero embryonic development / dendritic spine / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / PDZ domain / Pdz3 Domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PDZ domain / PDZ domain profile. ...Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / PDZ domain / Pdz3 Domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta A4 precursor protein-binding family A member 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsShen, Y. / Long, J. / Yan, X. / Xie, X.
CitationJournal: J Mol Cell Biol / Year: 2013
Title: Open-closed motion of Mint2 regulates APP metabolism
Authors: Xie, X. / Yan, X. / Wang, Z. / Zhou, H. / Diao, W. / Zhou, W. / Long, J. / Shen, Y.
History
DepositionJul 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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 A member 2


Theoretical massNumber of molelcules
Total (without water)42,5531
Polymers42,5531
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.662, 111.662, 84.586
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-45-

HOH

21A-53-

HOH

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Components

#1: Protein Amyloid beta A4 precursor protein-binding family A member 2 / Adapter protein X11beta / Neuron-specific X11L protein / Neuronal Munc18-1-interacting protein 2 / Mint-2


Mass: 42552.945 Da / Num. of mol.: 1 / Fragment: residues 365-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Mint2 / Production host: Escherichia coli (E. coli) / References: UniProt: O35431
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 3.58 Å3/Da / Density % sol: 65.62 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 38% P400 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→31.83 Å / Num. all: 16282 / Num. obs: 15588 / % possible obs: 91.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 37.9 Å2
Reflection shellResolution: 2.7→2.75 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQC

1aqc


Resolution: 2.7→31.83 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 120752.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.289 759 4.9 %RANDOM
Rwork0.265 ---
obs0.265 15588 91.4 %-
all-16282 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.1874 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 82 Å2
Baniso -1Baniso -2Baniso -3
1-12.48 Å20 Å20 Å2
2--12.48 Å20 Å2
3----24.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.7→31.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 0 51 2185
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.612
X-RAY DIFFRACTIONc_scbond_it3.962
X-RAY DIFFRACTIONc_scangle_it6.372.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.053 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.441 69 3.9 %
Rwork0.366 1681 -
obs--62.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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