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- PDB-3gnu: Toxin fold as basis for microbial attack and plant defense -

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Basic information

Entry
Database: PDB / ID: 3gnu
TitleToxin fold as basis for microbial attack and plant defense
Components25 kDa protein elicitor
KeywordsTOXIN / phytopathogenic / oomycete
Function / homologyNecrosis inducing protein / Necrosis inducing protein (NPP1) / killing of cells of another organism / extracellular region / metal ion binding / GUANIDINE / 25 kDa protein elicitor
Function and homology information
Biological speciesPythium aphanidermatum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsOttmann, C. / Luberacki, B. / Kuefner, I. / Koch, W. / Brunner, F. / Weyand, M. / Mattinen, L. / Pirhonen, M. / Anderluh, G. / Seitz, H.U. ...Ottmann, C. / Luberacki, B. / Kuefner, I. / Koch, W. / Brunner, F. / Weyand, M. / Mattinen, L. / Pirhonen, M. / Anderluh, G. / Seitz, H.U. / Nuernberger, T. / Oecking, C.
Citation
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Purification, crystallization and preliminary X-ray diffraction analysis of an oomycete-derived Nep1-like protein.
Authors: Luberacki, B. / Weyand, M. / Seitz, U. / Koch, W. / Oecking, C. / Ottmann, C.
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5144
Polymers23,3601
Non-polymers1543
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.940, 51.940, 175.034
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11P-416-

HOH

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Components

#1: Protein 25 kDa protein elicitor / Nep1-like proteins


Mass: 23359.971 Da / Num. of mol.: 1 / Fragment: UNP residues 22-234
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pythium aphanidermatum (eukaryote) / Plasmid: pQE60 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9SPD4
#2: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M HEPES-NaOH, 5.0M NaCl, 2% DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU MICROMAX-007 HF11.5418
SYNCHROTRONSLS X10SA20.97644, 0.97936, 0.96862
Detector
TypeIDDetectorDateDetails
MAR scanner 345 mm plate1IMAGE PLATEAug 2, 2005Osmic VariMaxHF mirror
MARMOSAIC 225 mm CCD2CCDOct 23, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
20.976441
30.979361
40.968621
ReflectionNumber: 143611 / Rmerge(I) obs: 0.072 / D res high: 2.1 Å / Num. obs: 27871 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
2.12.236249910.338
2.22.5772199.510.209
2.53697599.810.094
34554899.910.059
45198199.810.056
5686699.810.056
61093699.410.052
101517797.810.053
15254355.110.053
ReflectionResolution: 1.9→25 Å / Num. all: 19827 / Num. obs: 19306 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 25.481 Å2 / Rmerge(I) obs: 0.044
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.7 / Num. measured obs: 10994 / Num. unique all: 2501 / Num. unique obs: 2501 / Rsym value: 0.331 / % possible all: 90.1

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3.006data extraction
MAR345dtbdata collection
XDSdata reduction
SnBphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→24.9 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.161 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 965 5 %RANDOM
Rwork0.179 ---
obs0.181 19294 100 %-
all-19825 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.39 Å2 / Biso mean: 20.16 Å2 / Biso min: 7.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refine analyzeLuzzati coordinate error obs: 0.195 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 9 234 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221752
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.9352399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9275229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80625.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92415272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.883155
X-RAY DIFFRACTIONr_chiral_restr0.1020.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021387
X-RAY DIFFRACTIONr_nbd_refined0.2090.2927
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21213
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.211
X-RAY DIFFRACTIONr_mcbond_it0.7961.51113
X-RAY DIFFRACTIONr_mcangle_it1.28821762
X-RAY DIFFRACTIONr_scbond_it2.1083742
X-RAY DIFFRACTIONr_scangle_it3.0554.5629
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 62 -
Rwork0.221 1188 -
all-1250 -
obs--100 %

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