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Yorodumi- PDB-3g7v: Islet Amyloid Polypeptide (IAPP or Amylin) fused to Maltose Bindi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3g7v | |||||||||
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Title | Islet Amyloid Polypeptide (IAPP or Amylin) fused to Maltose Binding Protein | |||||||||
Components | Maltose-binding periplasmic protein, Islet amyloid polypeptide fusion protein | |||||||||
Keywords | Sugar binding protein / Hormone / native fold for amyloidogenic protein / Sugar transport / Transport / Amidation / Amyloid / Cleavage on pair of basic residues / Secreted | |||||||||
Function / homology | Function and homology information : / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / detection of maltose stimulus / maltose transport complex / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling ...: / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of amyloid fibril formation / negative regulation of bone resorption / eating behavior / detection of maltose stimulus / maltose transport complex / negative regulation of osteoclast differentiation / positive regulation of protein kinase A signaling / carbohydrate transport / Regulation of gene expression in beta cells / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of protein-containing complex assembly / positive regulation of calcium-mediated signaling / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / bone resorption / sensory perception of pain / ATP-binding cassette (ABC) transporter complex / osteoclast differentiation / cell chemotaxis / hormone activity / cell-cell signaling / amyloid-beta binding / outer membrane-bounded periplasmic space / G alpha (s) signalling events / positive regulation of MAPK cascade / periplasmic space / receptor ligand activity / positive regulation of apoptotic process / Amyloid fiber formation / signaling receptor binding / lipid binding / apoptotic process / DNA damage response / signal transduction / extracellular space / extracellular region / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.86 Å | |||||||||
Authors | Wiltzius, J.J.W. / Sawaya, M.R. / Eisenberg, D. | |||||||||
Citation | Journal: Protein Sci. / Year: 2009 Title: Atomic structures of IAPP (amylin) fusions suggest a mechanism for fibrillation and the role of insulin in the process Authors: Wiltzius, J.J. / Sievers, S.A. / Sawaya, M.R. / Eisenberg, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3g7v.cif.gz | 330.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3g7v.ent.gz | 268 KB | Display | PDB format |
PDBx/mmJSON format | 3g7v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3g7v_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 3g7v_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 3g7v_validation.xml.gz | 63.3 KB | Display | |
Data in CIF | 3g7v_validation.cif.gz | 91.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g7/3g7v ftp://data.pdbj.org/pub/pdb/validation_reports/g7/3g7v | HTTPS FTP |
-Related structure data
Related structure data | 3g7wC 1mpdS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 44442.172 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: malE, b4034, JW3994, IAPP / Plasmid: pMal-a1 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AEX9, UniProt: P10997 #2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.93 Å3/Da / Density % sol: 58.07 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2.0 M Ammonium Sulfate, 0.1M Sodium Acetate pH 4.6, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 28, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→90 Å / Num. all: 169517 / Num. obs: 169517 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.054 / Χ2: 1.09 / Net I/σ(I): 27.432 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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Phasing MR | Model details: Phaser MODE: MR_AUTO |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1MPD Resolution: 1.86→73.92 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.219 / WRfactor Rwork: 0.186 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.887 / SU B: 4.943 / SU ML: 0.071 / SU R Cruickshank DPI: 0.118 / SU Rfree: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.31 Å2 / Biso mean: 20.269 Å2 / Biso min: 6.02 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→73.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.905 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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