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- PDB-5wot: NMR solution structure of a-lytic protease using two 4D-spectra -

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Basic information

Entry
Database: PDB / ID: 5wot
TitleNMR solution structure of a-lytic protease using two 4D-spectra
ComponentsAlpha-lytic proteaseAlpha-lytic endopeptidase
KeywordsHYDROLASE / protease
Function / homology
Function and homology information


alpha-lytic endopeptidase / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Alpha-lytic protease prodomain / Streptogrisin prodomain / Peptidase S1A, alpha-lytic prodomain / Alpha-lytic protease prodomain / Peptidase S1A, streptogrisin / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Alpha-lytic protease
Similarity search - Component
Biological speciesLysobacter enzymogenes (bacteria)
MethodSOLUTION NMR / na
AuthorsEvangelidis, T. / Nerli, S. / Sgourakis, N.G. / Tripsianes, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI112573 United States
National Institutes of Health/Office of the DirectorS10OD018455 United States
CitationJournal: Nat Commun / Year: 2018
Title: Automated NMR resonance assignments and structure determination using a minimal set of 4D spectra.
Authors: Evangelidis, T. / Nerli, S. / Novacek, J. / Brereton, A.E. / Karplus, P.A. / Dotas, R.R. / Venditti, V. / Sgourakis, N.G. / Tripsianes, K.
History
DepositionAug 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other / Category: database_2 / pdbx_database_status / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-lytic protease


Theoretical massNumber of molelcules
Total (without water)19,8751
Polymers19,8751
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8160 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Alpha-lytic protease / Alpha-lytic endopeptidase / Alpha-lytic endopeptidase


Mass: 19875.131 Da / Num. of mol.: 1 / Fragment: residues 200-397 / Source method: isolated from a natural source / Source: (natural) Lysobacter enzymogenes (bacteria) / References: UniProt: P00778, alpha-lytic endopeptidase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic14D HC(CC-TOCSY(CO))NH
121isotropic14D 13C,15N edited HMQC-NOESY-HSQC
131isotropic14D 13C,13C edited HMQC-NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 2.0 mM [U-13C; U-15N] alpha-lytic protease protein, 92% H2O/8% D2O
Label: 13C_15N_sample / Solvent system: 92% H2O/8% D2O
SampleConc.: 2.0 mM / Component: alpha-lytic protease protein / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 50 mM / Label: conditions_1 / pH: 4.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 950 MHz

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Processing

NMR software
NameDeveloperClassification
4D-CHAINSEvangelidis and Tripsianeschemical shift assignment
CS-ROSETTAShen, Vernon, Baker and Baxrefinement
CS-ROSETTAShen, Vernon, Baker and Baxdata analysis
SparkyGoddardpeak picking
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
RefinementMethod: na / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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