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- PDB-4fco: Crystal structure of bace1 with its inhibitor -

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Basic information

Entry
Database: PDB / ID: 4fco
TitleCrystal structure of bace1 with its inhibitor
ComponentsBeta-secretase 1
KeywordsHydrolase/Hydrolase Inhibitor / HYDROLASE / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / protein processing / recycling endosome / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-0U4 / UREA / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsChen, T.T. / Chen, W.Y. / Li, L. / Xu, Y.C.
CitationJournal: To be Published / Year: 2012
Title: Flexibility of the Flap in the Active Site of BACE1 as Revealed by Crystal Structures and MD simulations
Authors: Xu, Y.C. / Chen, W.Y. / Chen, T.T. / Li, L.
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3717
Polymers48,2231
Non-polymers1,1486
Water7,927440
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Beta-secretase 1
hetero molecules

A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,74214
Polymers96,4462
Non-polymers2,29712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3520 Å2
ΔGint-83 kcal/mol
Surface area29860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.440, 128.420, 76.270
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-745-

HOH

21A-978-

HOH

Detailsbiological unit is the same as asym.

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Components

#1: Protein Beta-secretase 1 / Aspartyl protease 2 / ASP2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta- ...Aspartyl protease 2 / ASP2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP cleaving enzyme 1 / Memapsin-2 / Membrane-associated aspartic protease 2


Mass: 48222.922 Da / Num. of mol.: 1 / Mutation: K136A, E138A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1, KIAA1149 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-0U4 / N-[(2S,3R)-4-{[2-(1-benzylpiperidin-4-yl)ethyl]amino}-3-hydroxy-1-phenylbutan-2-yl]-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide


Mass: 739.966 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H53N5O5S
#4: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH4N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.7 M Li2SO4/100 mM HEPES, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.76→43.09 Å / Num. all: 51066 / Num. obs: 51092 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.112 / Net I/σ(I): 23.46
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.76-1.810.5335.27199.9
1.81-1.860.4396.551100
1.86-1.910.3687.921100
1.91-1.970.3019.711100
1.97-2.030.23912.511100
2.03-2.10.21114.481100
2.1-2.180.18116.771100
2.18-2.270.15619.07199.9
2.27-2.370.15620.721100
2.37-2.490.14522.71100
2.49-2.620.12925.751100
2.62-2.780.11129.48199.9
2.78-2.970.09534.571100
2.97-3.210.07640.831100
3.21-3.520.0747.171100
3.52-3.940.06251.4199.9
3.94-4.540.0656.84199.9
4.54-5.570.05456.61199.8
5.57-7.870.07353.651100
7.870.09458.33198.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→43.088 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.15 / σ(F): 2 / Phase error: 16.64 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1831 2552 5 %
Rwork0.1626 --
obs0.1636 51051 99.93 %
all-51092 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.867 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3373 Å20 Å20 Å2
2--0.2034 Å2-0 Å2
3---0.1338 Å2
Refinement stepCycle: LAST / Resolution: 1.76→43.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 76 440 3434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063074
X-RAY DIFFRACTIONf_angle_d1.1184179
X-RAY DIFFRACTIONf_dihedral_angle_d15.0571091
X-RAY DIFFRACTIONf_chiral_restr0.076451
X-RAY DIFFRACTIONf_plane_restr0.005535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.79390.2321390.20162642X-RAY DIFFRACTION100
1.7939-1.83050.22161400.18112663X-RAY DIFFRACTION100
1.8305-1.87030.20461410.17942667X-RAY DIFFRACTION100
1.8703-1.91380.21891400.16382667X-RAY DIFFRACTION100
1.9138-1.96170.18821410.16292675X-RAY DIFFRACTION100
1.9617-2.01470.19851420.14972691X-RAY DIFFRACTION100
2.0147-2.0740.17961390.15072653X-RAY DIFFRACTION100
2.074-2.14090.17261410.15262676X-RAY DIFFRACTION100
2.1409-2.21750.20211400.14792663X-RAY DIFFRACTION100
2.2175-2.30620.18261420.15612701X-RAY DIFFRACTION100
2.3062-2.41120.17221420.16162679X-RAY DIFFRACTION100
2.4112-2.53830.19521410.16362681X-RAY DIFFRACTION100
2.5383-2.69730.17841410.17152689X-RAY DIFFRACTION100
2.6973-2.90550.20771420.17512703X-RAY DIFFRACTION100
2.9055-3.19780.1671440.17262729X-RAY DIFFRACTION100
3.1978-3.66040.17181430.15172707X-RAY DIFFRACTION100
3.6604-4.61080.1511450.13782752X-RAY DIFFRACTION100
4.6108-43.10120.18971490.18552861X-RAY DIFFRACTION100

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