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- PDB-6wpg: Structural Basis of Salicylic Acid Perception by Arabidopsis NPR ... -

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Basic information

Entry
Database: PDB / ID: 6wpg
TitleStructural Basis of Salicylic Acid Perception by Arabidopsis NPR Proteins
ComponentsRegulatory protein NPR4
KeywordsPLANT PROTEIN / NPR4 / Arabidopsis / Salicylic acid / SA / receptor / plant immunity
Function / homology
Function and homology information


regulation of salicylic acid mediated signaling pathway / regulation of jasmonic acid mediated signaling pathway / salicylic acid binding / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / response to fungus / defense response to fungus / response to bacterium / protein ubiquitination / defense response to bacterium ...regulation of salicylic acid mediated signaling pathway / regulation of jasmonic acid mediated signaling pathway / salicylic acid binding / systemic acquired resistance / systemic acquired resistance, salicylic acid mediated signaling pathway / response to fungus / defense response to fungus / response to bacterium / protein ubiquitination / defense response to bacterium / identical protein binding / nucleus
Similarity search - Function
NPR1/NIM1-like, C-terminal / Regulatory protein NPR, central domain / Regulatory protein NPR / Domain of unknown function (DUF3420) / NPR1/NIM1 like defence protein C terminal / Domain of unknown function DUF3447 / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain ...NPR1/NIM1-like, C-terminal / Regulatory protein NPR, central domain / Regulatory protein NPR / Domain of unknown function (DUF3420) / NPR1/NIM1 like defence protein C terminal / Domain of unknown function DUF3447 / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / Regulatory protein NPR4
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.283 Å
AuthorsWang, W. / Withers, J. / Li, H. / Zwack, P.J. / Rusnac, D.V. / Shi, H. / Liu, L. / Yan, S. / Hinds, T.R. / Guttman, M. ...Wang, W. / Withers, J. / Li, H. / Zwack, P.J. / Rusnac, D.V. / Shi, H. / Liu, L. / Yan, S. / Hinds, T.R. / Guttman, M. / Dong, X. / Zheng, N.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2020
Title: Structural basis of salicylic acid perception by Arabidopsis NPR proteins.
Authors: Wang, W. / Withers, J. / Li, H. / Zwack, P.J. / Rusnac, D.V. / Shi, H. / Liu, L. / Yan, S. / Hinds, T.R. / Guttman, M. / Dong, X. / Zheng, N.
History
DepositionApr 27, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 21, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: Regulatory protein NPR4
B: Regulatory protein NPR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3294
Polymers41,0532
Non-polymers2762
Water1,36976
1
A: Regulatory protein NPR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6652
Polymers20,5261
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Regulatory protein NPR4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6652
Polymers20,5261
Non-polymers1381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.293, 88.293, 138.003
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Regulatory protein NPR4 / BTB/POZ domain-containing protein NPR4


Mass: 20526.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: NPR4, At4g19660, T16H5.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5ICL9
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.25 M potassium phosphate dibasic, 23% PEG 3350, pH 9.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.283→50 Å / Num. obs: 28861 / % possible obs: 100 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.02 / Rrim(I) all: 0.067 / Χ2: 0.906 / Net I/σ(I): 17.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.29-2.378.40.77128280.9510.2740.820.893100
2.37-2.479.80.50528630.9810.1660.5320.992100
2.47-2.5810.50.34228090.9890.1090.360.939100
2.58-2.7210.60.30728650.9860.0980.3230.844100
2.72-2.8910.70.19228520.9960.0610.2021.023100
2.89-3.1110.80.11928530.9980.0380.1251.024100
3.11-3.42110.07128930.9990.0220.0750.938100
3.42-3.9211.30.0728950.9980.0220.0730.548100
3.92-4.9311.60.06229450.9980.0190.0650.963100
4.93-5011.10.033305810.010.0350.92199.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.283→39.418 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.07
RfactorNum. reflection% reflection
Rfree0.2238 1428 4.97 %
Rwork0.2051 --
obs0.2061 28714 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 203.58 Å2 / Biso mean: 79.6069 Å2 / Biso min: 41.01 Å2
Refinement stepCycle: final / Resolution: 2.283→39.418 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 30 76 1961
Biso mean--58.37 82.16 -
Num. residues----225
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.283-2.36460.31671460.2696258796
2.3646-2.45920.23191350.2337270699
2.4592-2.57120.24341340.21922672100
2.5712-2.70670.24761480.23252721100
2.7067-2.87620.3061500.24492694100
2.8762-3.09820.28871390.23922719100
3.0982-3.40980.27551440.21292746100
3.4098-3.90290.22881190.18532768100
3.9029-4.91570.16971530.17712783100
4.9157-39.4180.21191600.2095289099
Refinement TLS params.Method: refined / Origin x: 40.3332 Å / Origin y: 34.0584 Å / Origin z: 44.7081 Å
111213212223313233
T0.5208 Å20.0117 Å20.0716 Å2-0.4591 Å20.0228 Å2--0.441 Å2
L1.49 °2-0.5978 °21.8778 °2-1.4735 °2-1.5738 °2--4.2282 °2
S0.0513 Å °0.2082 Å °0.1105 Å °0.0702 Å °-0.1357 Å °-0.1234 Å °-0.1967 Å °0.3101 Å °0.143 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-7 - 512
2X-RAY DIFFRACTION1allB371 - 512
3X-RAY DIFFRACTION1allS1
4X-RAY DIFFRACTION1allS2
5X-RAY DIFFRACTION1allW1 - 76

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