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- PDB-5utg: Red abalone lysin F104A -

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Basic information

Entry
Database: PDB / ID: 5utg
TitleRed abalone lysin F104A
ComponentsEgg-lysin
KeywordsCELL ADHESION / fertilization protein
Function / homology
Function and homology information


acrosomal lumen / single fertilization
Similarity search - Function
Fertilization protein / Egg lysin (Sperm-lysin) / Egg-lysin superfamily / Egg lysin (Sperm-lysin) / Lysin / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHaliotis rufescens (red abalone)
MethodSOLUTION NMR / simulated annealing
AuthorsWilburn, D.B. / Tuttle, L.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R01-HD076862 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM116298 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Solution structure of sperm lysin yields novel insights into molecular dynamics of rapid protein evolution.
Authors: Wilburn, D.B. / Tuttle, L.M. / Klevit, R.E. / Swanson, W.J.
History
DepositionFeb 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Dec 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 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Egg-lysin


Theoretical massNumber of molelcules
Total (without water)16,0901
Polymers16,0901
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10270 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Egg-lysin / Sperm-lysin


Mass: 16089.939 Da / Num. of mol.: 1 / Fragment: UNP residues 19-152 / Mutation: F104A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliotis rufescens (red abalone) / Plasmid: pET11d / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P04552

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D 1H-15N NOESY
131isotropic13D 1H-15N TOCSY
141isotropic13D 1H-15N hetNOE
151isotropic12D 1H-15N T1
161isotropic12D 1H-15N T2
172isotropic13D HNHA
1102isotropic23D HNCO
182isotropic23D HNCA
1172isotropic23D HN(CO)CA
1162isotropic23D HN(CA)CB
1152isotropic23D HN(COCA)CB
1142isotropic23D (H)CCH-TOCSY
1132isotropic23D (H)CCH-COSY
1122isotropic23D 1H-13C NOESY aliphatic
1112isotropic23D 1H-13C NOESY aromatic
193anisotropic22D 1H-15N HSQC-IPAP
1182isotropic22D 1H-13C HSQC aliphatic
1192isotropic22D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1300 uM [U-15N] lysin, 200 mM natural abundunce sodium chloride, 10 mM sodium phosphate, 93% H2O/7% D2O15N_sample93% H2O/7% D2O
solution2300 uM [U-13C; U-15N] lysin, 200 mM sodium chloride, 10 mM sodium phosphate, 93% H2O/7% D2O13C15N_sample93% H2O/7% D2O
solution3300 uM [U-15N] lysin, 5 w/v c12e6/hexanol, 200 mM sodium chloride, 10 mM sodium phosphate, 93% H2O/7% D2O15N_c12e693% H2O/7% D2ORDC sample, 5% w/v c12e6/hexanol as alignment media.
solution4200 uM [U-13C; U-15N] lysin, 200 mM sodium chloride, 10 mM Tris, 93% H2O/7% D2OATCUN_lysin93% H2O/7% D2O13C,15N labelled ATCUN tagged sample. Cu2SO4 titrated in up to 1:1 ratio.
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMlysin[U-15N]1
200 mMsodium chloridenatural abundunce1
10 mMsodium phosphatenatural abundance1
300 uMlysin[U-13C; U-15N]2
200 mMsodium chloridenatural abundance2
10 mMsodium phosphatenatural abundance2
300 uMlysin[U-15N]3
5 w/vc12e6/hexanolnatural abundance3
200 mMsodium chloridenatural abundance3
10 mMsodium phosphatenatural abundance3
200 uMlysin[U-13C; U-15N]4
200 mMsodium chloridenatural abundance4
10 mMTrisnatural abundance4
Sample conditionsIonic strength: 200 mM NaCl mM / Label: standard_condition / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCEBrukerAVANCE5001
Bruker AVANCEBrukerAVANCE6002Cryo Probe

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
X-PLOR NIH2.43Schwieters, Kuszewski, Tjandra and Clorerefinement
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TopSpinBruker Biospincollection
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure calculation
X-PLOR NIH2.43Schwieters, Kuszewski, Tjandra and Clorestructure calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 2
Details: torsion angle dynamics, molecular dynamics. The flexible Gly0 residue is left out of the coordinates, since it is unrestrained and not present in the native sequence of red abalone lysin.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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