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- PDB-4xbh: Soluble rabbit neprilysin -

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Basic information

Entry
Database: PDB / ID: 4xbh
TitleSoluble rabbit neprilysin
ComponentsNeprilysin
KeywordsHYDROLASE / Neutral Endopeptidase / Proteinase / Zn-dependent
Function / homology
Function and homology information


neprilysin / creatinine metabolic process / substance P catabolic process / peptide metabolic process / cellular response to UV-A / hormone catabolic process / bradykinin catabolic process / neuron projection terminus / cellular response to UV-B / amyloid-beta clearance ...neprilysin / creatinine metabolic process / substance P catabolic process / peptide metabolic process / cellular response to UV-A / hormone catabolic process / bradykinin catabolic process / neuron projection terminus / cellular response to UV-B / amyloid-beta clearance / cellular response to cytokine stimulus / brush border / replicative senescence / amyloid-beta metabolic process / sensory perception of pain / kidney development / peptide binding / protein processing / metalloendopeptidase activity / synaptic vesicle / axon / synapse / dendrite / proteolysis / zinc ion binding / 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
PHOSPHATE ION / Neprilysin
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.114 Å
AuthorsLabiuk, S.L. / Grochulski, P. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, Canada) Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2019
Title: Structures of soluble rabbit neprilysin complexed with phosphoramidon or thiorphan.
Authors: Labiuk, S.L. / Sygusch, J. / Grochulski, P.
History
DepositionDec 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _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_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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 2.1Sep 27, 2023Group: 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
B: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,64113
Polymers158,9592
Non-polymers2,68211
Water27,1311506
1
A: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9317
Polymers79,4791
Non-polymers1,4526
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Neprilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7106
Polymers79,4791
Non-polymers1,2305
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-80 kcal/mol
Surface area57500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.361, 108.142, 212.784
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Neprilysin / / Atriopeptidase / Enkephalinase / Neutral endopeptidase 24.11 / Neutral endopeptidase / Skin ...Atriopeptidase / Enkephalinase / Neutral endopeptidase 24.11 / Neutral endopeptidase / Skin fibroblast elastase / SFE


Mass: 79479.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: MME / Production host: Pichia pastoris (fungus) / Strain (production host): GS115 / Variant (production host): his4- / References: UniProt: P08049, neprilysin

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Sugars , 2 types, 7 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / 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 , 3 types, 1510 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1506 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsThe sequence from GB XP_008264403.1 matches the experimental electron density

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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: 2.51 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7 / Details: PEG 4000, magnesium chloride, cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 1999 / Details: Brandeis B4 detector
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 88988 / % possible obs: 94.4 % / Redundancy: 4.96 % / Biso Wilson estimate: 20.07 Å2 / Rmerge(I) obs: 0.056 / Χ2: 0.982 / Net I/av σ(I): 26.268 / Net I/σ(I): 16 / Num. measured all: 441341
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-IDRejects% possible all
2.1-2.180.11758940.7561063.3
2.18-2.260.12587300.9191093.9
2.26-2.370.09689020.8951095.6
2.37-2.490.0891110.9391097.4
2.49-2.650.07191450.9751098
2.65-2.850.06692021.041098.2
2.85-3.140.05493061.1121098.7
3.14-3.590.05293821.1011099.4
3.59-4.520.0594960.9941099.4
4.52-500.04698200.9151099.2

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Processing

Software
NameVersionClassification
HKL-20001.12.ddata scaling
PHENIX1.9-1692refinement
Coot0.7.2model building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dmt

1dmt


Resolution: 2.114→39.601 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2113 1999 2.25 %
Rwork0.166 86866 -
obs0.167 88865 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.38 Å2 / Biso mean: 25.7871 Å2 / Biso min: 4.41 Å2
Refinement stepCycle: final / Resolution: 2.114→39.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11182 0 166 1506 12854
Biso mean--48.22 32.41 -
Num. residues----1392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311607
X-RAY DIFFRACTIONf_angle_d0.68415712
X-RAY DIFFRACTIONf_chiral_restr0.0281707
X-RAY DIFFRACTIONf_plane_restr0.0032042
X-RAY DIFFRACTIONf_dihedral_angle_d12.2784294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1136-2.16650.26041110.17544830494176
2.1665-2.2250.23441400.17636065620595
2.225-2.29050.26161340.19525873600792
2.2905-2.36440.21781410.1796161630297
2.3644-2.44890.23481440.1746196634097
2.4489-2.54690.24311440.1766267641198
2.5469-2.66280.22251450.17546301644698
2.6628-2.80320.23941440.17686286643098
2.8032-2.97880.23341470.17526347649499
2.9788-3.20870.22711450.18516361650699
3.2087-3.53140.2151490.16596426657599
3.5314-4.04190.18441480.14846467661599
4.0419-5.09070.16161520.137765566708100
5.0907-39.60770.19981550.16216730688599

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