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- PDB-5no9: NLPPya in complex with mannosamine -

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Basic information

Entry
Database: PDB / ID: 5no9
TitleNLPPya in complex with mannosamine
Components25 kDa protein elicitor
KeywordsTOXIN / Actinoporin-like proteins / Nep1-like proteins / Complex with hexose
Function / homologyNecrosis inducing protein / Necrosis inducing protein (NPP1) / killing of cells of another organism / metal ion binding / 2-amino-2-deoxy-alpha-D-mannopyranose / 25 kDa protein elicitor
Function and homology information
Biological speciesPythium aphanidermatum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsPodobnik, M. / Anderluh, G. / Lenarcic, T.
Funding support Slovenia, 2items
OrganizationGrant numberCountry
Slovenian Research AgencyJ1-7515 Slovenia
Slovenian Research AgencyP1-0391 Slovenia
CitationJournal: Science / Year: 2017
Title: Eudicot plant-specific sphingolipids determine host selectivity of microbial NLP cytolysins.
Authors: Lenarcic, T. / Albert, I. / Bohm, H. / Hodnik, V. / Pirc, K. / Zavec, A.B. / Podobnik, M. / Pahovnik, D. / Zagar, E. / Pruitt, R. / Greimel, P. / Yamaji-Hasegawa, A. / Kobayashi, T. / ...Authors: Lenarcic, T. / Albert, I. / Bohm, H. / Hodnik, V. / Pirc, K. / Zavec, A.B. / Podobnik, M. / Pahovnik, D. / Zagar, E. / Pruitt, R. / Greimel, P. / Yamaji-Hasegawa, A. / Kobayashi, T. / Zienkiewicz, A. / Gomann, J. / Mortimer, J.C. / Fang, L. / Mamode-Cassim, A. / Deleu, M. / Lins, L. / Oecking, C. / Feussner, I. / Mongrand, S. / Anderluh, G. / Nurnberger, T.
History
DepositionApr 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Structure summary / Category: entity / Item: _chem_comp.name / _entity.pdbx_description
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)96,8089
Polymers96,5314
Non-polymers2765
Water14,520806
1
A: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1572
Polymers24,1331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1572
Polymers24,1331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1572
Polymers24,1331
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 25 kDa protein elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3363
Polymers24,1331
Non-polymers2032
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.026, 122.284, 121.138
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-567-

HOH

21B-600-

HOH

31D-593-

HOH

41D-594-

HOH

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Components

#1: Protein
25 kDa protein elicitor


Mass: 24132.787 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pythium aphanidermatum (eukaryote) / Gene: SD21-1 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9SPD4
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-95Z / 2-amino-2-deoxy-alpha-D-mannopyranose / alpha-D-mannosamine / 2-amino-2-deoxy-alpha-D-mannose / 2-amino-2-deoxy-D-mannose / 2-amino-2-deoxy-mannose


Type: D-saccharide, alpha linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DManpNaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranosamineCOMMON NAMEGMML 1.0
a-D-ManpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 / Details: PEG 4000 MgCl2 Tris Glycerol Methanol

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid nitrogen
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 16, 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: 1.75→36.586 Å / Num. obs: 85931 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.68 % / Biso Wilson estimate: 20.96 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.117 / Χ2: 0.975 / Net I/σ(I): 11.63
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.856.7110.8052.19135580.8090.87198.3
1.85-1.986.5430.4933.64129330.9160.53699.6
1.98-2.146.6820.2946.2120990.9620.31999.7
2.14-2.346.980.1869.57111740.9840.299.8
2.34-2.626.7680.13812.33101420.990.1599.9
2.62-3.026.2570.09416.5989560.9940.10399.9
3.02-3.76.990.06424.6576460.9970.06999.9
3.7-5.216.4760.05629.5659790.9970.06199.9
5.21-36.5866.6060.05429.5434440.9970.05999.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.34 Å43.03 Å
Translation6.34 Å43.03 Å

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Processing

Software
NameVersionClassification
XSCALEVERSION March 1, 2015data scaling
PHASER2.5.6phasing
PHENIX1.11.1refinement
PDB_EXTRACT3.22data extraction
XDSVERSION March 1, 2015data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GNU truncated

3gnu


Resolution: 1.75→36.586 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2031 1995 2.32 %
Rwork0.1745 --
obs0.1752 85899 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.63 Å2 / Biso mean: 24.0616 Å2 / Biso min: 11.72 Å2
Refinement stepCycle: final / Resolution: 1.75→36.586 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6417 0 16 806 7239
Biso mean--60.22 30.15 -
Num. residues----829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066621
X-RAY DIFFRACTIONf_angle_d0.8089020
X-RAY DIFFRACTIONf_chiral_restr0.051947
X-RAY DIFFRACTIONf_plane_restr0.0061179
X-RAY DIFFRACTIONf_dihedral_angle_d4.0734262
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7475-1.79120.27391350.27795764589997
1.7912-1.83970.28661220.23845940606299
1.8397-1.89380.24871620.2195906606899
1.8938-1.95490.24391340.20525971610599
1.9549-2.02480.26971400.207159256065100
2.0248-2.10580.21911540.188359826136100
2.1058-2.20170.21741310.173259836114100
2.2017-2.31770.20491520.177159576109100
2.3177-2.46290.22661390.177160126151100
2.4629-2.6530.2091380.184360086146100
2.653-2.91990.20261490.179260346183100
2.9199-3.34220.20871420.164860626204100
3.3422-4.20980.17121450.146661026247100
4.2098-36.59370.16081520.154962586410100
Refinement TLS params.Method: refined / Origin x: -22.177 Å / Origin y: -31.7584 Å / Origin z: -29.5598 Å
111213212223313233
T0.1366 Å2-0.0037 Å20.0088 Å2-0.1457 Å20.0045 Å2--0.1443 Å2
L0.0197 °2-0.0327 °20.006 °2-0.072 °20.0719 °2--0.0558 °2
S0.0117 Å °-0.005 Å °-0.0001 Å °0.0005 Å °-0.0144 Å °0.0124 Å °0.0026 Å °-0.0203 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 213
2X-RAY DIFFRACTION1allA301
3X-RAY DIFFRACTION1allB1 - 213
4X-RAY DIFFRACTION1allB301
5X-RAY DIFFRACTION1allC1 - 213
6X-RAY DIFFRACTION1allC301
7X-RAY DIFFRACTION1allD1 - 213
8X-RAY DIFFRACTION1allD301 - 302
9X-RAY DIFFRACTION1allS1 - 806

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