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- PDB-6mm4: Solution NMR Structure of Engineered Cystine Knot Protein 2.5F -

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Basic information

Entry
Database: PDB / ID: 6mm4
TitleSolution NMR Structure of Engineered Cystine Knot Protein 2.5F
ComponentsEngineered Cystine Knot Protein 2.5F
KeywordsPROTEIN BINDING / Cystine Knot / Knottin / Protein Engineering
Biological speciessynthetic construct (others)
MethodSOLUTION NMR / molecular dynamics
AuthorsCochran, F.V. / Cochran, J.R.
CitationJournal: To be published
Title: Solution NMR Structure of Engineered Cystine Knot Protein 2.5F
Authors: Cochran, F.V. / Cochran, J.R.
History
DepositionSep 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: 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 9, 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: Engineered Cystine Knot Protein 2.5F


Theoretical massNumber of molelcules
Total (without water)3,3001
Polymers3,3001
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area2840 Å2
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 Engineered Cystine Knot Protein 2.5F


Mass: 3299.699 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)
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
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D C(CO)NH
151isotropic13D HNCO
161isotropic13D HN(CA)CB
171isotropic13D H(CCO)NH
181isotropic13D 1H-15N NOESY
191isotropic13D 1H-13C NOESY aliphatic
1101isotropic13D 1H-13C NOESY aromatic
1111isotropic2GHNCO LRA

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Sample preparation

DetailsType: solution / Contents: 400 uM [U-13C; U-15N] 2.5F, 95% H2O/5% D2O / Details: 50 mM sodium phosphate / Label: sample / Solvent system: 95% H2O/5% D2O
SampleConc.: 400 uM / Component: 2.5F / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 50 mM sodium phosphate / Ionic strength: 50 mM / Label: conditions_1 / 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
NameDeveloperClassification
YASARAYASARA Biosciences GmbHrefinement
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
RefinementMethod: molecular dynamics / Software ordinal: 1 / Details: REFINEMENT IN EXPLICIT SOLVENT
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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