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- PDB-5nnw: NLPPya in complex with glucosamine -

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Basic information

Entry
Database: PDB / ID: 5nnw
TitleNLPPya in complex with glucosamine
Components25 kDa protein elicitor
KeywordsTOXIN / Actinoporin-like proteins / Nep1-like proteins / Complex
Function / homologyNecrosis inducing protein / Necrosis inducing protein (NPP1) / killing of cells of another organism / metal ion binding / 2-amino-2-deoxy-beta-D-glucopyranose / 25 kDa protein elicitor
Function and homology information
Biological speciesPythium aphanidermatum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.54 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 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 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
Water12,989721
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
MethodPISA
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
MethodPISA
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
MethodPISA
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
MethodPISA
Unit cell
Length a, b, c (Å)114.996, 122.285, 121.099
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
11A-578-

HOH

21A-580-

HOH

31D-550-

HOH

41D-575-

HOH

51D-577-

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 BL21(DE3) (bacteria) / 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-GCS / 2-amino-2-deoxy-beta-D-glucopyranose / beta-D-glucosamine / 2-amino-2-deoxy-beta-D-glucose / 2-amino-2-deoxy-D-glucose / 2-amino-2-deoxy-glucose / D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 179.171 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13NO5
IdentifierTypeProgram
DGlcpNbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 44.22 %
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: 1.54→36.621 Å / Num. obs: 123312 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.205 % / Biso Wilson estimate: 17.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.065 / Χ2: 1.008 / Net I/σ(I): 17.75 / Num. measured all: 765186
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.54-1.634.3570.5452.267853820176180270.7940.61889.3
1.63-1.756.2080.3664.3911756118947189370.9320.499.9
1.75-1.896.7230.2098.3911863617650176450.9820.227100
1.89-2.076.3220.12413.5310257016265162240.9920.13599.7
2.07-2.316.7850.07821.439998914753147360.9970.08499.9
2.31-2.676.610.05927.28616113056130340.9980.06499.8
2.67-3.266.3790.04335.427074711107110900.9980.04799.8
3.26-4.66.7940.03646.2358838866786600.9990.03999.9
4.6-36.6216.4820.03347.132146497249590.9990.03699.7

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3gnu


Resolution: 1.54→36.621 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 2008 1.63 %
Rwork0.1733 121270 -
obs0.1737 123278 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.01 Å2 / Biso mean: 20.7437 Å2 / Biso min: 10.32 Å2
Refinement stepCycle: final / Resolution: 1.54→36.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6404 0 16 721 7141
Biso mean--44.95 27.5 -
Num. residues----826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066610
X-RAY DIFFRACTIONf_angle_d0.839008
X-RAY DIFFRACTIONf_chiral_restr0.052946
X-RAY DIFFRACTIONf_plane_restr0.0071177
X-RAY DIFFRACTIONf_dihedral_angle_d3.1134096
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 (%)
1.5402-1.57880.32121190.26597236735582
1.5788-1.62140.25741440.23898173831794
1.6214-1.66920.22131430.227687198862100
1.6692-1.7230.24861390.196687658904100
1.723-1.78460.18751490.177587718920100
1.7846-1.85610.19691460.172187388884100
1.8561-1.94050.20071410.169687938934100
1.9405-2.04280.19691440.178187498893100
2.0428-2.17080.18981510.168687698920100
2.1708-2.33840.19281420.176488188960100
2.3384-2.57370.2051410.179988298970100
2.5737-2.94590.18411410.177688518992100
2.9459-3.7110.18461550.160889069061100
3.711-36.6310.17541530.154991539306100
Refinement TLS params.Method: refined / Origin x: 13.9644 Å / Origin y: 22.9588 Å / Origin z: -7.1382 Å
111213212223313233
T0.1203 Å2-0.0108 Å20.0135 Å2-0.1225 Å2-0.0068 Å2--0.1255 Å2
L0.0414 °2-0.038 °20.053 °2-0.0938 °2-0.0651 °2--0.112 °2
S0.0125 Å °0.0039 Å °0.0148 Å °0.0083 Å °-0.0099 Å °-0.024 Å °-0.0037 Å °-0.0056 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 - 721

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