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- PDB-2hiz: Crystal Structure of human beta-secretase (BACE) in the presence ... -

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Basic information

Entry
Database: PDB / ID: 2hiz
TitleCrystal Structure of human beta-secretase (BACE) in the presence of an inhibitor
ComponentsBeta-secretase 1
KeywordsHYDROLASE / protein-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 / recycling endosome / protein processing / 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-LIJ / PHOSPHATE ION / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBenson, T.E. / Prince, D.B. / Tomasselli, A.G. / Emmons, T.L. / Paddock, D.J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: Design of potent inhibitors of human beta-secretase. Part 1.
Authors: Freskos, J.N. / Fobian, Y.M. / Benson, T.E. / Bienkowski, M.J. / Brown, D.L. / Emmons, T.L. / Heintz, R. / Laborde, A. / McDonald, J.J. / Mischke, B.V. / Molyneaux, J.M. / Moon, J.B. / ...Authors: Freskos, J.N. / Fobian, Y.M. / Benson, T.E. / Bienkowski, M.J. / Brown, D.L. / Emmons, T.L. / Heintz, R. / Laborde, A. / McDonald, J.J. / Mischke, B.V. / Molyneaux, J.M. / Moon, J.B. / Mullins, P.B. / Bryan Prince, D. / Paddock, D.J. / Tomasselli, A.G. / Winterrowd, G.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
B: Beta-secretase 1
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,0409
Polymers150,7523
Non-polymers2,2886
Water4,143230
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1084
Polymers50,2511
Non-polymers8583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9182
Polymers50,2511
Non-polymers6681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0133
Polymers50,2511
Non-polymers7632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.240, 104.090, 100.950
Angle α, β, γ (deg.)90.000, 103.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 50250.586 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-LIJ / BENZYL [(1S)-2-({(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}AMINO)-2-OXO-1-{[(1-PROPYLBUTYL)SULFONYL]METHYL}ETHYL]CARBAMATE


Mass: 667.855 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H49N3O7S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growDetails: 1.0M ammonium phosphate, 0.1M ammonium citrate pH 5.6, 293 K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 51993 / % possible obs: 91.3 % / Rmerge(I) obs: 0.06 / Χ2: 0.613 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.590.34656850.36899.9
2.59-2.690.37456340.71299.9
2.69-2.820.256800.415100
2.82-2.960.13656860.413100
2.96-3.150.09556810.484100
3.15-3.390.07456440.557100
3.39-3.730.12923791.24141.7
3.73-4.270.04341160.90772.3
4.27-5.380.02957230.829100
5.38-500.02457650.6999.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / FOM work R set: 0.814 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.253 5007 8.8 %
Rwork0.214 --
obs-49480 86.5 %
Displacement parametersBiso mean: 40.988 Å2
Baniso -1Baniso -2Baniso -3
1-4.302 Å20 Å2-0.628 Å2
2---9.051 Å20 Å2
3---4.749 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8790 0 156 230 9176
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.504
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_scbond_it1.8962
X-RAY DIFFRACTIONc_mcangle_it2.4572
X-RAY DIFFRACTIONc_scangle_it2.9192.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.5-2.520.396570.317591648
2.52-2.530.4021140.3229221036
2.53-2.550.3291230.3099001023
2.55-2.570.4351140.339361050
2.57-2.590.3821130.3349281041
2.59-2.610.3681090.309886995
2.61-2.630.36890.315910999
2.63-2.650.329870.308883970
2.65-2.670.3451170.2879581075
2.67-2.690.3461010.3088991000
2.69-2.720.307950.3169361031
2.72-2.740.3021130.2759401053
2.74-2.760.371820.2759621044
2.76-2.790.3321150.2769661081
2.79-2.810.3641250.2719571082
2.81-2.840.3421000.2529521052
2.84-2.870.3261050.2559801085
2.87-2.90.2861130.2569701083
2.9-2.930.2871030.2449951098
2.93-2.960.31250.23310001125
2.96-30.2931100.2399721082
3-3.030.3151120.24410031115
3.03-3.070.3171230.24310111134
3.07-3.110.2971180.2329461064
3.11-3.150.2911180.23910311149
3.15-3.190.2921000.259911091
3.19-3.240.3051020.24210151117
3.24-3.280.2521090.22510111120
3.28-3.340.2961180.229701088
3.34-3.390.2841070.2389881095
3.39-3.450.281180.23810031121
3.45-3.510.251160.2259341050
3.51-3.580.299260.217248274
3.58-3.65
3.65-3.730.70820.6152426
3.73-3.820.237690.201545614
3.82-3.910.241700.196580650
3.91-4.010.205340.192278312
4.01-4.130.2111260.17710121138
4.13-4.260.1841170.16310091126
4.26-4.410.1971170.15410391156
4.41-4.590.186970.15410421139
4.59-4.80.1541170.12810251142
4.8-5.040.2111060.16410451151
5.04-5.350.1971320.18110221154
5.35-5.760.2411110.20710471158
5.76-6.320.2321140.18810441158
6.32-7.20.21000.210511151
7.2-8.930.1871150.18310491164
8.93-200.2061030.19710671170
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.paramMSI_CNX_TOPPAR:protein.top
X-RAY DIFFRACTION2MSI_CNX_TOPPAR:dna-rna_rep.paramMSI_CNX_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:water_rep.paramMSI_CNX_TOPPAR:water.top
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:ion.paramMSI_CNX_TOPPAR:ion.top
X-RAY DIFFRACTION5lig.parlig.top

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