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- PDB-2ksw: Backbone 1H, 13C, and 15N Chemical Shift Assignments for Oryctin -

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Basic information

Entry
Database: PDB / ID: 2ksw
TitleBackbone 1H, 13C, and 15N Chemical Shift Assignments for Oryctin
ComponentsOryctin
KeywordsHYDROLASE INHIBITOR / Kazal-type / PROTEASE INHIBITOR
Function / homologyDna Ligase; domain 1 - #260 / Dna Ligase; domain 1 / 2-Layer Sandwich / Alpha Beta / Oryctin
Function and homology information
Biological speciesOryctes rhinoceros (rhinoceros beetle)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model 1
AuthorsHorita, S. / Ishibashi, J. / Nagata, K. / Miyakawa, T. / Yamakawa, M. / Tanokura, M.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Isolation, cDNA cloning, and structure-based functional characterization of oryctin, a hemolymph protein from the coconut rhinoceros beetle, Oryctes rhinoceros, as a novel serine protease inhibitor
Authors: Horita, S. / Ishibashi, J. / Nagata, K. / Miyakawa, T. / Yamakawa, M. / Tanokura, M.
History
DepositionJan 14, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Database references / Other / Category: database_2 / pdbx_database_status / Item: _pdbx_database_status.status_code_cs
Revision 1.3Jun 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oryctin


Theoretical massNumber of molelcules
Total (without water)7,2571
Polymers7,2571
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 / 200target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Oryctin


Mass: 7257.395 Da / Num. of mol.: 1 / Fragment: UNP residues 20-85
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctes rhinoceros (rhinoceros beetle) / Production host: Escherichia coli (E. coli) / References: UniProt: O96050

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D HN(CO)CA
1813D H(CCO)NH
1913D (H)CCH-TOCSY
11013D 1H-15N NOESY
11113D (H)CCH-COSY
11213D 1H-13C NOESY

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Sample preparation

DetailsContents: 2 mM [U-100% 13C; U-100% 15N] oryctin-1, 100 mM sodium chloride-2, 10 % D2O-3, 90 % H2O-4, 50 mM sodium phosphate-5, 0.02 w/v sodium azide-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMoryctin-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
10 %D2O-31
90 %H2O-41
50 mMsodium phosphate-51
0.02 w/vsodium azide-61
Sample conditionsIonic strength: 0.1 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 500 MHz

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Processing

NMR softwareName: CYANA / Developer: Guntert P. / Classification: refinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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