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- PDB-1aun: PATHOGENESIS-RELATED PROTEIN 5D FROM NICOTIANA TABACUM -

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Basic information

Entry
Database: PDB / ID: 1aun
TitlePATHOGENESIS-RELATED PROTEIN 5D FROM NICOTIANA TABACUM
ComponentsPR-5D
KeywordsANTIFUNGAL PROTEIN / PATHOGENESIS-RELATED PROTEIN / PR-5D / OSMOTIN / THAUMATIN-LIKE PROTEIN
Function / homology
Function and homology information


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
Similarity search - Component
Biological speciesNicotiana tabacum (common tobacco)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKoiwa, H. / Kato, H. / Nakatsu, T. / Oda, J. / Yamada, Y. / Sato, F.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of tobacco PR-5d protein at 1.8 A resolution reveals a conserved acidic cleft structure in antifungal thaumatin-like proteins.
Authors: Koiwa, H. / Kato, H. / Nakatsu, T. / Oda, J. / Yamada, Y. / Sato, F.
#1: Journal: Plant Cell.Physiol. / Year: 1997
Title: Purification and Characterization of Tobacco Pathogenesis-Related Protein Pr-5D, an Antifungal Thaumatin-Like Protein
Authors: Koiwa, H. / Kato, H. / Nakatsu, T. / Oda, J. / Yamada, Y. / Sato, F.
History
DepositionAug 29, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PR-5D


Theoretical massNumber of molelcules
Total (without water)22,7791
Polymers22,7791
Non-polymers00
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.140, 63.690, 45.610
Angle α, β, γ (deg.)90.00, 107.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PR-5D / OSMOTIN-LIKE PROTEIN


Mass: 22778.502 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nicotiana tabacum (common tobacco) / Cell: CULTURED CELL / Cellular location: VACUOLE / Strain: SAMSUN NN / References: UniProt: P25871
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.45 Å3/Da / Density % sol: 50 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 0.7 M MGCL2, 10% GLYCEROL, 50 MM HEPES, PH 7.5
Crystal grow
*PLUS
Method: other / Details: Koiwa, H., (1997) Plant Cell Physiol., 38, 783.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.61 Å / Num. obs: 21635 / % possible obs: 75.3 % / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 11
Reflection shellResolution: 1.61→1.7 Å / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 2 / % possible all: 31

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Processing

Software
NameVersionClassification
PROCESSdata collection
PROCESSdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
PROCESSdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1THV

1thv


Resolution: 1.8→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.219 841 4.8 %RANDOM
Rwork0.169 ---
obs0.169 17471 86.1 %-
Displacement parametersBiso mean: 25.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 0 89 1685
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.17
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.611.5
X-RAY DIFFRACTIONx_mcangle_it3.532
X-RAY DIFFRACTIONx_scbond_it4.752
X-RAY DIFFRACTIONx_scangle_it7.182.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 112 4.8 %
Rwork0.252 2206 -
obs--68.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.17

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