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- PDB-2la1: Expression in Pichia pastoris and backbone dynamics of dendroaspi... -

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Basic information

Entry
Database: PDB / ID: 2la1
TitleExpression in Pichia pastoris and backbone dynamics of dendroaspin, a three finger toxin
ComponentsMambin
KeywordsTOXIN / dendroaspin / disintegrin / integrin / three-finger fold / snake toxin
Function / homologySnake three-finger toxin / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / toxin activity / extracellular region / Mainly Beta / Dendroaspin
Function and homology information
Biological speciesDendroaspis jamesoni kaimosae (eastern Jameson's mamba)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailsclosest to the average, model 2
AuthorsChuang, W.J. / Cheng, C.H. / Chen, Y.C. / Shiu, J.H.
CitationJournal: Protein Sci. / Year: 2012
Title: Dynamics and functional differences between dendroaspin and rhodostomin: Insights into protein scaffolds in integrin recognition
Authors: Cheng, C.H. / Chen, Y.C. / Shiu, J.H. / Chang, Y.T. / Chang, Y.S. / Huang, C.H. / Chen, C.Y. / Chuang, W.J.
History
DepositionMar 1, 2011Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
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 / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Nov 6, 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: Mambin


Theoretical massNumber of molelcules
Total (without water)6,7621
Polymers6,7621
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Mambin / Dendroaspin / Glycoprotein IIb-IIIa antagonist / Platelet aggregation inhibitor


Mass: 6761.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dendroaspis jamesoni kaimosae (eastern Jameson's mamba)
Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P28375
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H NOESY
1212D 1H-1H TOCSY
1322D 1H-15N HSQC
1423D 1H-15N NOESY
1523D 1H-15N TOCSY
1623D HNHA

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Sample preparation

Details
Solution-IDContentsSolvent system
13.18 mM H2O-1, 90% H2O/10% D2O90% H2O/10% D2O
21.92 mM [U-98% 15N] H2O-2, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
3.18 mMH2O-11
1.92 mMH2O-2[U-98% 15N]2
Sample conditionspH: 4 / Pressure: ambient / Temperature: 300 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMRBruker Biospincollection
AURELIANeidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerpeak picking
AURELIANeidig, Geyer, Gorler, Antz, Saffrich, Beneicke, Kalbitzerchemical shift assignment
X-PLOR3.85Brungerrefinement
X-PLOR NIHrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 777 / NOE intraresidue total count: 69 / NOE long range total count: 271 / NOE medium range total count: 249 / NOE sequential total count: 105 / Disulfide bond constraints total count: 4 / Hydrogen bond constraints total count: 21 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 58 / Protein psi angle constraints total count: 0
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: lowest energy / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0 Å / Representative conformer: 2
NMR ensemble rmsDistance rms dev: 1.25 Å / Distance rms dev error: 0.44 Å

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