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- PDB-5ycz: Crystal structure of Alocasin, protease inhibitor from Giant Taro... -

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Basic information

Entry
Database: PDB / ID: 5ycz
TitleCrystal structure of Alocasin, protease inhibitor from Giant Taro (Arum macrorrhizon)
ComponentsTrypsin/chymotrypsin inhibitor
KeywordsPLANT PROTEIN / Protease inhibitor / Storage protein / Tubers / Alocasia / Alocasin / Kunitz type
Function / homologyProteinase inhibitor A/B / Proteinase inhibitor I3, Kunitz legume / Trypsin and protease inhibitor / Soybean trypsin inhibitor (Kunitz) family of protease inhibitors / Kunitz inhibitor STI-like superfamily / serine-type endopeptidase inhibitor activity / Trypsin/chymotrypsin inhibitor
Function and homology information
Biological speciesAlocasia macrorrhizos (giant taro)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsVajravijayan, S. / Pletnev, S. / Nandhagopal, N. / Gunasekaran, K.
CitationJournal: Pest Manag. Sci. / Year: 2018
Title: Crystal structure of a novel Kunitz type inhibitor, alocasin with anti-Aedes aegypti activity targeting midgut proteases.
Authors: Vajravijayan, S. / Pletnev, S. / Pletnev, V.Z. / Nandhagopal, N. / Gunasekaran, K.
History
DepositionSep 8, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 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 / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trypsin/chymotrypsin inhibitor
B: Trypsin/chymotrypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)39,5862
Polymers39,5862
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-13 kcal/mol
Surface area16110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.446, 51.446, 298.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Trypsin/chymotrypsin inhibitor


Mass: 19793.139 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Alocasia macrorrhizos (giant taro) / References: UniProt: P35812
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES (pH7.5). 1.6 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 14759 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.042 / Rrim(I) all: 0.104 / Χ2: 0.89 / Net I/σ(I): 8.4 / Num. measured all: 83766
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.5940.82314010.5560.4220.9370.68497.9
2.59-2.694.80.71614420.6120.3430.8030.70599.6
2.69-2.825.60.64414200.7550.2950.7140.696100
2.82-2.966.20.44614370.8630.1990.4910.729100
2.96-3.156.30.33414690.9150.1470.3670.75299.9
3.15-3.396.20.18914680.960.0830.2070.81199.8
3.39-3.736.20.12414660.9710.0540.1361.01299.5
3.73-4.275.90.09114990.9810.040.11.30998.5
4.27-5.385.80.06514740.9770.0290.0721.22997.6
5.38-305.70.04416830.9940.020.0490.84299

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→29.354 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2989 680 5 %RANDOM
Rwork0.2174 ---
obs0.2215 13596 91.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.12 Å2 / Biso mean: 41.3613 Å2 / Biso min: 13.5 Å2
Refinement stepCycle: final / Resolution: 2.502→29.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2636 0 0 102 2738
Biso mean---38.82 -
Num. residues----350

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