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Yorodumi- PDB-8ulm: Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ulm | ||||||
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Title | Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide NCR13: Solution NMR structure of the isomer with C4:C23, C15:C30, and C10:C28 disulfide bonds | ||||||
Components | Nodule cysteine-rich protein 13 | ||||||
Keywords | ANTIFUNGAL PROTEIN / antifunal activity / ENDOSYMBIOTIC / DISULFIDE-RICH / ANTIMICROBIAL PROTEIN / NCR peptide | ||||||
Function / homology | Late nodulin / Late nodulin domain / metal ion binding / Nodule cysteine-rich protein 13 Function and homology information | ||||||
Biological species | Cicer arietinum (chickpea) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Buchko, G.W. / Zhou, M. / Shah, D.M. / Velivelli, S.L.S. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Solution NMR structures of the Chickpea (Cicer arientinum) nodule-specific cysteine-rich peptide NCR13 in two different disulfide bonding patterns Authors: Buchko, G.W. / Zhou, M. / Velivelli, S.L.S. / Shah, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ulm.cif.gz | 235.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ulm.ent.gz | 196.2 KB | Display | PDB format |
PDBx/mmJSON format | 8ulm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ulm_validation.pdf.gz | 531.6 KB | Display | wwPDB validaton report |
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Full document | 8ulm_full_validation.pdf.gz | 709.8 KB | Display | |
Data in XML | 8ulm_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | 8ulm_validation.cif.gz | 31.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ul/8ulm ftp://data.pdbj.org/pub/pdb/validation_reports/ul/8ulm | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3741.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cicer arietinum (chickpea) / Gene: NCR13 / Production host: Komagataella pastoris (fungus) / References: UniProt: A0A0U8SNQ0 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 70 mM / Ionic strength err: 2 / Label: 1 / pH: 5.3 / PH err: 0.1 / Pressure: 1 atm / Temperature: 293 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 3 Details: It was not possible to verify the disulfide bonding pattern using mass spectrometry or other methods. Therefore the alphafold predicted disulfide pattern was used in the structure ...Details: It was not possible to verify the disulfide bonding pattern using mass spectrometry or other methods. Therefore the alphafold predicted disulfide pattern was used in the structure calculations. The structure was first solved using CYANA and then refined in explicit water adding 10% to the upper bound of the NOE restraints. | ||||||||||||||||||||||||||||
NMR representative | Selection criteria: closest to the average | ||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 |