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- PDB-2m99: Solution structure of a chymotrypsin inhibitor from the Taiwan cobra -

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Basic information

Entry
Database: PDB / ID: 2m99
TitleSolution structure of a chymotrypsin inhibitor from the Taiwan cobra
ComponentsProtease inhibitor NACI
KeywordsHYDROLASE INHIBITOR / Naja naja atra / chymotrypsin inhibitor / NACI
Function / homology
Function and homology information


serine-type endopeptidase inhibitor activity / extracellular region
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Kunitz-type serine protease inhibitor NACI
Similarity search - Component
Biological speciesNaja atra (Chinese cobra)
MethodSOLUTION NMR / minimization
Model detailslowest energy, model1
AuthorsLin, Y.-J. / Ikeya, T. / Guntert, P. / Chang, L.-S.
CitationJournal: Molecules / Year: 2013
Title: NMR solution structure of a Chymotrypsin inhibitor from the Taiwan cobra Naja naja atra.
Authors: Lin, Y.J. / Ikeya, T. / Guntert, P. / Chang, L.S.
History
DepositionJun 5, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protease inhibitor NACI


Theoretical massNumber of molelcules
Total (without water)6,3971
Polymers6,3971
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 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Protease inhibitor NACI / Chymotrypsin inhibitor / NACI


Mass: 6397.058 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja atra (Chinese cobra) / Gene: aci / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZPJ7

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D HN(CA)CB
1213D CBCA(CO)NH
1313D HN(CA)CO
1413D HCACO
1513D HBHA(CO)NH
1612D 1H-15N HSQC
1713D C(CO)NH
1813D (H)CCH-TOCSY
1912D CB(CGCD)HD
11012D CB(CGCDCE)HE
11113D 1H-15N NOESY
11212D 1H-1H NOESY

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Sample preparation

DetailsContents: 1.5 mM [U-13C; U-15N] NACI-1, 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1.5 mM / Component: NACI-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0.05 / pH: 3.0 / Pressure: ambient / Temperature: 295 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
SparkyGoddarddata analysis
VnmrJVarianprocessing
OPAL1.4Luginbuhl, Guntert, Billeter and Wuthrichgeometry optimization
OPALrefinement
RefinementMethod: minimization / Software ordinal: 1
NMR constraintsHydrogen bond constraints total count: 24 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 36 / Protein psi angle constraints total count: 38
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 2 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 3 ° / Maximum upper distance constraint violation: 5 Å / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.092 Å

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