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- PDB-6gid: High resolution crystal structure of substrate-free human neprilysin -

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Basic information

Entry
Database: PDB / ID: 6gid
TitleHigh resolution crystal structure of substrate-free human neprilysin
ComponentsNeprilysin
KeywordsHYDROLASE / Substrate-free
Function / homology
Function and homology information


neuropeptide processing / neprilysin / creatinine metabolic process / oligopeptidase activity / exopeptidase activity / substance P catabolic process / Physiological factors / cellular response to UV-A / peptide metabolic process / amyloid-beta clearance by cellular catabolic process ...neuropeptide processing / neprilysin / creatinine metabolic process / oligopeptidase activity / exopeptidase activity / substance P catabolic process / Physiological factors / cellular response to UV-A / peptide metabolic process / amyloid-beta clearance by cellular catabolic process / hormone catabolic process / bradykinin catabolic process / cardiolipin binding / neuron projection terminus / positive regulation of neurogenesis / cellular response to UV-B / amyloid-beta clearance / phosphatidylserine binding / cellular response to cytokine stimulus / brush border / replicative senescence / amyloid-beta metabolic process / Metabolism of Angiotensinogen to Angiotensins / sensory perception of pain / secretory granule membrane / kidney development / positive regulation of long-term synaptic potentiation / lung development / peptide binding / trans-Golgi network / protein catabolic process / placenta development / protein processing / metalloendopeptidase activity / response to estrogen / synaptic vesicle / presynapse / cytoplasmic vesicle / endopeptidase activity / learning or memory / early endosome / membrane raft / axon / focal adhesion / neuronal cell body / synapse / dendrite / Neutrophil degranulation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / zinc ion binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Neprilysin-like (M13) protease domain profile. / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Collagenase (Catalytic Domain) ...Neutral endopeptidase; domain 2 / Neutral endopeptidase , domain2 / Neprilysin-like (M13) protease domain profile. / Peptidase M13 / Peptidase M13, N-terminal domain / Peptidase M13, C-terminal domain / Peptidase M13, domain 2 / Peptidase family M13 / Peptidase family M13 / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Neprilysin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMoss, S. / Subramanian, V. / Acharya, K.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private286 (AS-PhD2015b006) United Kingdom
CitationJournal: J. Struct. Biol. / Year: 2018
Title: High resolution crystal structure of substrate-free human neprilysin.
Authors: Moss, S. / Subramanian, V. / Acharya, K.R.
History
DepositionMay 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,47819
Polymers79,5261
Non-polymers1,95218
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-5 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.424, 107.424, 112.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-909-

HOH

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein Neprilysin / Atriopeptidase / Common acute lymphocytic leukemia antigen / CALLA / Enkephalinase / Neutral ...Atriopeptidase / Common acute lymphocytic leukemia antigen / CALLA / Enkephalinase / Neutral endopeptidase 24.11 / Neutral endopeptidase / Skin fibroblast elastase / SFE


Mass: 79525.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MME, EPN / Production host: Komagataella pastoris (fungus) / References: UniProt: P08473, neprilysin
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 7 types, 477 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M potassium nitrate and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.9→93.032 Å / Num. obs: 59422 / % possible obs: 100 % / Redundancy: 53.7 % / Net I/σ(I): 25.3
Reflection shellResolution: 1.9→1.94 Å

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Processing

Software
NameClassification
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JMY

5jmy


Resolution: 1.9→93.032 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 24.22
RfactorNum. reflection% reflection
Rfree0.2354 3000 5.05 %
Rwork0.1899 --
obs0.1921 59376 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→93.032 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5543 0 118 463 6124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095775
X-RAY DIFFRACTIONf_angle_d0.8947811
X-RAY DIFFRACTIONf_dihedral_angle_d7.5423430
X-RAY DIFFRACTIONf_chiral_restr0.054847
X-RAY DIFFRACTIONf_plane_restr0.0061014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93120.36561430.34882629X-RAY DIFFRACTION100
1.9312-1.96450.3171330.31272663X-RAY DIFFRACTION100
1.9645-2.00030.35151400.28562659X-RAY DIFFRACTION100
2.0003-2.03870.30981710.27282635X-RAY DIFFRACTION100
2.0387-2.08040.31781480.25472646X-RAY DIFFRACTION100
2.0804-2.12560.28771320.22582679X-RAY DIFFRACTION100
2.1256-2.1750.27541480.21322624X-RAY DIFFRACTION100
2.175-2.22940.24011310.19842703X-RAY DIFFRACTION100
2.2294-2.28970.25861650.1972650X-RAY DIFFRACTION100
2.2897-2.35710.25091100.19262678X-RAY DIFFRACTION100
2.3571-2.43320.25691540.19922649X-RAY DIFFRACTION100
2.4332-2.52020.26511210.20212694X-RAY DIFFRACTION100
2.5202-2.62110.25781360.19632701X-RAY DIFFRACTION100
2.6211-2.74040.24811430.20912660X-RAY DIFFRACTION100
2.7404-2.88490.27331620.20922674X-RAY DIFFRACTION100
2.8849-3.06560.28741540.21952676X-RAY DIFFRACTION100
3.0656-3.30230.24251280.19722717X-RAY DIFFRACTION100
3.3023-3.63470.2271570.18312688X-RAY DIFFRACTION100
3.6347-4.16060.20661370.15292728X-RAY DIFFRACTION100
4.1606-5.24190.15491450.14112745X-RAY DIFFRACTION100
5.2419-93.14360.19041420.16032878X-RAY DIFFRACTION100

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