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- PDB-6lek: Tertiary structure of Barnacle cement protein MrCP20 -

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Basic information

Entry
Database: PDB / ID: 6lek
TitleTertiary structure of Barnacle cement protein MrCP20
ComponentsCement protein-20k
KeywordsSTRUCTURAL PROTEIN / Barnacle cement protein / Megabalanus rosa.
Function / homologymulticellular organism adhesion / extracellular region / Cement protein 20
Function and homology information
Biological speciesMegabalanus rosa (acorn barnacle)
MethodSOLUTION NMR / simulated annealing
AuthorsMohanram, H.
CitationJournal: Philos.Trans.R.Soc.Lond.B Biol.Sci. / Year: 2019
Title: Three-dimensional structure of Megabalanus rosa Cement Protein 20 revealed by multi-dimensional NMR and molecular dynamics simulations.
Authors: Mohanram, H. / Kumar, A. / Verma, C.S. / Pervushin, K. / Miserez, A.
History
DepositionNov 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cement protein-20k


Theoretical massNumber of molelcules
Total (without water)21,4671
Polymers21,4671
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10790 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cement protein-20k


Mass: 21467.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megabalanus rosa (acorn barnacle) / Gene: cp-20k / Production host: Expression vector pET-mod (others) / References: UniProt: Q9GRC4
Has protein modificationY

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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 HNCA
131isotropic13D CBCA(CO)NH
141isotropic13D HNCO
151isotropic13D 1H-15N NOESY

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Sample preparation

DetailsType: solution
Contents: 20 mM TRIS, 150 mM sodium chloride, 90% H2O/10% D2O
Label: 15N_13C / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMTRISnatural abundance1
150 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 150 mM / Label: Conditions_1 / pH: 8.3 / Pressure: 1 bar / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
TopSpinBruker Biospincollection
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10 / Conformers submitted total number: 10

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