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- PDB-2m7t: Solution NMR Structure of Engineered Cystine Knot Protein 2.5D -

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Basic information

Entry
Database: PDB / ID: 2m7t
TitleSolution NMR Structure of Engineered Cystine Knot Protein 2.5D
ComponentsCystine Knot Protein 2.5D
KeywordsPROTEIN BINDING / Protein Engineering / Cystine Knot / Knottin / CASP
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
Model detailslowest energy, model1
AuthorsCochran, F.V. / Das, R.
CitationJournal: Proteins / Year: 2014
Title: Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10.
Authors: Kryshtafovych, A. / Moult, J. / Bales, P. / Bazan, J.F. / Biasini, M. / Burgin, A. / Chen, C. / Cochran, F.V. / Craig, T.K. / Das, R. / Fass, D. / Garcia-Doval, C. / Herzberg, O. / Lorimer, ...Authors: Kryshtafovych, A. / Moult, J. / Bales, P. / Bazan, J.F. / Biasini, M. / Burgin, A. / Chen, C. / Cochran, F.V. / Craig, T.K. / Das, R. / Fass, D. / Garcia-Doval, C. / Herzberg, O. / Lorimer, D. / Luecke, H. / Ma, X. / Nelson, D.C. / van Raaij, M.J. / Rohwer, F. / Segall, A. / Seguritan, V. / Zeth, K. / Schwede, T.
History
DepositionApr 30, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: 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:
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Assembly

Deposited unit
A: Cystine Knot Protein 2.5D


Theoretical massNumber of molelcules
Total (without water)3,2511
Polymers3,2511
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Cystine Knot Protein 2.5D


Mass: 3250.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
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-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D H(CCO)NH
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
1101ghnco LRA
11112D 1H-13C HSQC aromatic

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Sample preparation

DetailsContents: 300 uM [U-13C; U-15N] 2.5D, 50 mM sodium phosphate, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
300 uMEngineered Cystine Knot Protein[U-13C; U-15N]1
50 mMsodium phosphate1
Sample conditionsIonic strength: 50 / pH: 6 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS8001
Varian VNSVarianVNS6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
YASARArefinement
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: Refinement in explicit solvent
NMR constraintsNOE constraints total: 462 / NOE long range total count: 136 / NOE medium range total count: 78 / Disulfide bond constraints total count: 18 / Hydrogen bond constraints total count: 16 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 15 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 0 ° / Maximum upper distance constraint violation: 0.33 Å / Torsion angle constraint violation method: CYANA

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