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- PDB-6qbd: Crystal structure of NLPPya P41A, D44N, N48E mutant -

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Basic information

Entry
Database: PDB / ID: 6qbd
TitleCrystal structure of NLPPya P41A, D44N, N48E mutant
Components25 kDa protein elicitor
KeywordsTOXIN / NLP protein / mutant / beta-sandwich / Pythium aphanidermatum
Function / homologyNecrosis inducing protein / Necrosis inducing protein (NPP1) / killing of cells of another organism / metal ion binding / 25 kDa protein elicitor
Function and homology information
Biological speciesPythium aphanidermatum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLenarcic, T. / Podobnik, M. / Anderluh, G.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyP1-0391 Slovenia
Slovenian Research AgencyJ1-7515 Slovenia
CitationJournal: Plos Pathog. / Year: 2019
Title: Molecular basis for functional diversity among microbial Nep1-like proteins.
Authors: Lenarcic, T. / Pirc, K. / Hodnik, V. / Albert, I. / Borisek, J. / Magistrato, A. / Nurnberger, T. / Podobnik, M. / Anderluh, G.
History
DepositionDec 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 25 kDa protein elicitor
B: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6575
Polymers46,5842
Non-polymers733
Water7,458414
1
A: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3413
Polymers23,2921
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3162
Polymers23,2921
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.391, 87.391, 115.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

21B-451-

HOH

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Components

#1: Protein 25 kDa protein elicitor


Mass: 23291.896 Da / Num. of mol.: 2 / Mutation: P41A, D44N, N48E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pythium aphanidermatum (eukaryote) / Gene: SD21-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SPD4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3 M MgCl2, 0.1 M Tris/HCl pH 9, 10 % (v/v) glycerol, 5 % (v/v) methanol, 22 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 14, 2015
Details: a vertical collimating mirror, a double-crystal Si(111) monochromator, a bendable focussing mirror
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→42.284 Å / Num. obs: 33415 / % possible obs: 100 % / Redundancy: 13.024 % / Biso Wilson estimate: 18.64 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.225 / Rrim(I) all: 0.234 / Χ2: 1.02 / Net I/σ(I): 9.38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.94-2.0612.1980.7153.5253000.9250.746100
2.06-2.213.7830.4645.6549730.9680.482100
2.2-2.3813.6560.3836.846790.9770.398100
2.38-2.6113.370.337.7842950.9790.343100
2.61-2.9112.1920.2619.6639300.9830.273100
2.91-3.3613.4380.18913.5634880.9890.196100
3.36-4.1113.3230.16216.9229850.9870.168100
4.11-5.811.9520.1521723570.9890.159100
5.8-42.28412.7460.14418.2114080.9930.15199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation1.95 Å42.28 Å
Translation1.95 Å42.28 Å

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Processing

Software
NameVersionClassification
XSCALEVERSION Jan 26, 2018data scaling
PHASER2.7.16phasing
PHENIX1.11.1refinement
PDB_EXTRACT3.24data extraction
XDSVERSION Jan 26, 2018data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GNZ

3gnz


Resolution: 1.95→42.284 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.97
RfactorNum. reflection% reflection
Rfree0.2068 2000 5.99 %
Rwork0.1696 --
obs0.1718 33411 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 76.55 Å2 / Biso mean: 17.2826 Å2 / Biso min: 8.27 Å2
Refinement stepCycle: final / Resolution: 1.95→42.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3168 0 3 414 3585
Biso mean--24.31 21.39 -
Num. residues----409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073253
X-RAY DIFFRACTIONf_angle_d0.7594422
X-RAY DIFFRACTIONf_chiral_restr0.051467
X-RAY DIFFRACTIONf_plane_restr0.006577
X-RAY DIFFRACTIONf_dihedral_angle_d5.1021922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9501-1.99880.22851400.210721942334
1.9988-2.05290.22181400.177621952335
2.0529-2.11330.21961400.165221992339
2.1133-2.18150.20691400.168322142354
2.1815-2.25940.2421410.168222082349
2.2594-2.34990.24831410.1722142355
2.3499-2.45680.24481410.1722232364
2.4568-2.58640.21511420.179622232365
2.5864-2.74840.20491420.188422362378
2.7484-2.96050.21811420.17922382380
2.9605-3.25830.18521450.17522612406
3.2583-3.72960.2261440.161422662410
3.7296-4.69790.15641460.141122992445
4.6979-42.29370.19791560.176224412597
Refinement TLS params.Method: refined / Origin x: 22.1385 Å / Origin y: 20.5583 Å / Origin z: 21.0944 Å
111213212223313233
T0.1193 Å20.0005 Å2-0.0012 Å2-0.1134 Å2-0.0091 Å2--0.1363 Å2
L0.423 °2-0.0263 °20.0381 °2--0.1976 °2-0.0106 °2---0.022 °2
S-0.0089 Å °0.0647 Å °-0.0227 Å °-0.0003 Å °0.018 Å °-0.0011 Å °0.0082 Å °0.012 Å °0.0101 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 213
2X-RAY DIFFRACTION1allA301 - 302
3X-RAY DIFFRACTION1allB1 - 213
4X-RAY DIFFRACTION1allB301
5X-RAY DIFFRACTION1allS1 - 300
6X-RAY DIFFRACTION1allS301 - 351
7X-RAY DIFFRACTION1allS352 - 414

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