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- PDB-1sgz: Crystal Structure of Unbound Beta-Secretase Catalytic Domain. -

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Basic information

Entry
Database: PDB / ID: 1sgz
TitleCrystal Structure of Unbound Beta-Secretase Catalytic Domain.
ComponentsBeta-secretase
KeywordsHYDROLASE / beta-secretase / memapsin / BACE / aspartic protease / protease flap / drug design / Asp2 / Alzheimer's disease
Function / homology
Function and homology information


memapsin 2 / Golgi-associated vesicle lumen / beta-aspartyl-peptidase activity / signaling receptor ligand precursor processing / amyloid-beta formation / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / detection of mechanical stimulus involved in sensory perception of pain / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / beta-aspartyl-peptidase activity / signaling receptor ligand precursor processing / amyloid-beta formation / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / amyloid-beta metabolic process / detection of mechanical stimulus involved in sensory perception of pain / prepulse inhibition / cellular response to manganese ion / multivesicular body / presynaptic modulation of chemical synaptic transmission / protein serine/threonine kinase binding / cellular response to copper ion / hippocampal mossy fiber to CA3 synapse / trans-Golgi network / recycling endosome / protein processing / response to lead ion / cellular response to amyloid-beta / synaptic vesicle / late endosome / peptidase activity / positive regulation of neuron apoptotic process / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / early endosome / lysosome / endosome / endosome membrane / membrane raft / endoplasmic reticulum lumen / Amyloid fiber formation / axon / neuronal cell body / dendrite / enzyme binding / cell surface / Golgi apparatus / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHong, L. / Tang, J.
CitationJournal: Biochemistry / Year: 2004
Title: Flap Position of Free Memapsin 2 (beta-Secretase), a Model for Flap Opening in Aspartic Protease Catalysis
Authors: Hong, L. / Tang, J.
History
DepositionFeb 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-secretase
B: Beta-secretase
C: Beta-secretase
D: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)173,2514
Polymers173,2514
Non-polymers00
Water16,394910
1
A: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)43,3131
Polymers43,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)43,3131
Polymers43,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)43,3131
Polymers43,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-secretase


Theoretical massNumber of molelcules
Total (without water)43,3131
Polymers43,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.160, 130.812, 88.651
Angle α, β, γ (deg.)90.00, 97.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43312.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE, BACE1 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P56817, memapsin 2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 56.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 10, 2003 / Details: mirrors
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→42.73 Å / Num. all: 131206 / Num. obs: 124094 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.56 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.9 / Num. unique all: 12798 / % possible all: 98.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FKN

1fkn


Resolution: 2→42.7 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Simulated annealing refinement, maximum likelihood target using amplitudes.
RfactorNum. reflection% reflectionSelection details
Rfree0.228 9941 -RANDOM
Rwork0.196 ---
all0.196 131206 --
obs0.196 124094 94.6 %-
Displacement parametersBiso mean: 26.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12212 0 0 910 13122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.002
RfactorNum. reflection% reflection
Rfree0.228 9941 -
Rwork0.196 --
obs-124094 94.4 %

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