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- PDB-2i0w: Crystal structure analysis of NP24-I, a thaumatin-like protein -

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Basic information

Entry
Database: PDB / ID: 2i0w
TitleCrystal structure analysis of NP24-I, a thaumatin-like protein
ComponentsProtein NP24
KeywordsANTIFUNGAL PROTEIN / alpha-beta protein
Function / homology
Function and homology information


beta-glucanase activity / endo-1,3(4)-beta-glucanase / antifungal innate immune response / vacuole / response to salt stress / defense response / response to virus / killing of cells of another organism / cytoplasm
Similarity search - Function
Thaumatin / Thaumatin / Thaumatin, conserved site / Thaumatin family signature. / Thaumatin family / Thaumatin family / Thaumatin family profile. / Thaumatin family / Osmotin/thaumatin-like superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Osmotin-like protein NP24-I
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChakrabarti, C. / Ghosh, R.
CitationJournal: Planta / Year: 2008
Title: Crystal structure analysis of NP24-I: a thaumatin-like protein
Authors: Ghosh, R. / Chakrabarti, C.
History
DepositionAug 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein NP24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2682
Polymers22,2321
Non-polymers351
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.010, 61.010, 62.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Protein NP24 / Pathogenesis-related protein PR P23 / Salt-induced protein


Mass: 22232.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Ripe tomato / Source: (natural) Solanum lycopersicum (tomato) / References: UniProt: P12670
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1M lithium chloride, 20% PEG 3350, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 7, 2005 / Details: Osmic multilayers
RadiationMonochromator: osmic multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 8574 / % possible obs: 99.9 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 4.06 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 3.9
Reflection shellResolution: 2.45→2.51 Å / Redundancy: 4.04 % / Rmerge(I) obs: 0.3369 / Mean I/σ(I) obs: 1.5 / Num. unique all: 567 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
AUTOMARdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PCV

1pcv


Resolution: 2.5→19.83 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 988975.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.223 415 5.2 %RANDOM
Rwork0.171 ---
obs0.171 8035 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.1517 Å2 / ksol: 0.305957 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 1 67 1621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it3.731.5
X-RAY DIFFRACTIONc_mcangle_it5.752
X-RAY DIFFRACTIONc_scbond_it7.52
X-RAY DIFFRACTIONc_scangle_it10.482.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.238 -4.6 %
Rwork0.237 841 -
obs--62.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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