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- PDB-2ao7: Adam10 Disintegrin and cysteine- rich domain -

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Basic information

Entry
Database: PDB / ID: 2ao7
TitleAdam10 Disintegrin and cysteine- rich domain
ComponentsADAM 10
KeywordsHYDROLASE / Extracellular / protease / Disintegrin
Function / homology
Function and homology information


Degradation of the extracellular matrix / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse ...Degradation of the extracellular matrix / ADAM10 endopeptidase / constitutive protein ectodomain proteolysis / regulation of vasculature development / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Post-translational protein phosphorylation / epidermal growth factor receptor ligand maturation / monocyte activation / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / protein catabolic process at postsynapse / postsynapse organization / : / regulation of Notch signaling pathway / perinuclear endoplasmic reticulum / positive regulation of T cell chemotaxis / pore complex assembly / tetraspanin-enriched microdomain / metallodipeptidase activity / negative regulation of cell adhesion / adherens junction organization / regulation of postsynapse organization / Neutrophil degranulation / clathrin-coated vesicle / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Golgi-associated vesicle / cochlea development / pore complex / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / response to tumor necrosis factor / Notch signaling pathway / synaptic membrane / adherens junction / metalloendopeptidase activity / protein processing / SH3 domain binding / metallopeptidase activity / positive regulation of cell growth / endopeptidase activity / in utero embryonic development / postsynaptic density / axon / Golgi membrane / protein phosphorylation / negative regulation of gene expression / dendrite / glutamatergic synapse / positive regulation of cell population proliferation / protein kinase binding / Golgi apparatus / cell surface / protein homodimerization activity / metal ion binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin ...: / ADAM10, cysteine-rich domain / ADAM10/ADAM17 catalytic domain / Metallo-peptidase family M12B Reprolysin-like / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Disintegrin and metalloproteinase domain-containing protein 10
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsJanes, P.W. / Saha, N. / Barton, W.A. / Kolev, M.V. / Wimmer-Kleikamp, S.H. / Nievergall, E. / Blobel, C.P. / Himanen, J.-P. / Lackmann, M. / Nikolov, D.B.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2005
Title: Adam meets Eph: an ADAM substrate recognition module acts as a molecular switch for ephrin cleavage in trans.
Authors: Janes, P.W. / Saha, N. / Barton, W.A. / Kolev, M.V. / Wimmer-Kleikamp, S.H. / Nievergall, E. / Blobel, C.P. / Himanen, J.-P. / Lackmann, M. / Nikolov, D.B.
History
DepositionAug 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADAM 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0633
Polymers20,8711
Non-polymers1922
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: ADAM 10
hetero molecules

A: ADAM 10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1266
Polymers41,7412
Non-polymers3844
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation24_555-z+3/4,-y+3/4,-x+3/41
Buried area2750 Å2
ΔGint-53 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.780, 146.780, 146.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein ADAM 10 / / A disintegrin and metalloproteinase domain 10 / Mammalian disintegrin-metalloprotease / Myelin- ...A disintegrin and metalloproteinase domain 10 / Mammalian disintegrin-metalloprotease / Myelin-associated metalloproteinase / Kuzbanian protein homolog


Mass: 20870.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ADAM10, MADM / Cell line (production host): HEK 293 / Production host: Homo sapiens (human) / References: UniProt: Q10741, ADAM10 endopeptidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

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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: 3.15 Å3/Da / Density % sol: 61.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10 mM Hepes, 150 mM NaCl, 0.2M Ammonium Sulfate, 30% PEG 4000, soaked in 1 mM AuCl and 20% glycerol (cryoprotectant) , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 1.034, 0.9789, 1.016
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0341
20.97891
31.0161
ReflectionResolution: 2.9→8 Å / Num. obs: 11118 / % possible obs: 99.5 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
autoSHARPphasing
DMmodel building
CNSrefinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.289 544 random
Rwork0.261 --
obs-10100 -
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1099 0 10 0 1109

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