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- PDB-5ngo: Crystal structure of the PARP domain of Arabidopsis RADICAL-INDUC... -

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Basic information

Entry
Database: PDB / ID: 5ngo
TitleCrystal structure of the PARP domain of Arabidopsis RADICAL-INDUCED CELL DEATH1
ComponentsInactive poly [ADP-ribose] polymerase RCD1
KeywordsPLANT PROTEIN / inactive Poly-(ADP-ribose)-Polymerase / PARP
Function / homology
Function and homology information


lateral root morphogenesis / response to ethylene / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to ozone / embryo development ending in seed dormancy / response to water deprivation / programmed cell death / response to superoxide / regulation of reactive oxygen species metabolic process ...lateral root morphogenesis / response to ethylene / jasmonic acid mediated signaling pathway / ethylene-activated signaling pathway / response to ozone / embryo development ending in seed dormancy / response to water deprivation / programmed cell death / response to superoxide / regulation of reactive oxygen species metabolic process / response to osmotic stress / NAD+ ADP-ribosyltransferase activity / response to salt stress / nitric oxide biosynthetic process / nuclear matrix / defense response to bacterium / nucleus / cytoplasm
Similarity search - Function
Inactive poly [ADP-ribose] polymerase RCD1/SRO1-5 / RST domain / RCD1-SRO-TAF4 (RST) plant domain / RST domain profile. / WWE domain / WWE domain profile. / Poly(ADP-ribose) polymerase catalytic domain / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
Inactive poly [ADP-ribose] polymerase RCD1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsWirthmueller, L. / Banfield, M.J.
CitationJournal: New Phytol. / Year: 2018
Title: Arabidopsis downy mildew effector HaRxL106 suppresses plant immunity by binding to RADICAL-INDUCED CELL DEATH1.
Authors: Wirthmueller, L. / Asai, S. / Rallapalli, G. / Sklenar, J. / Fabro, G. / Kim, D.S. / Lintermann, R. / Jaspers, P. / Wrzaczek, M. / Kangasjarvi, J. / MacLean, D. / Menke, F.L.H. / Banfield, M.J. / Jones, J.D.G.
History
DepositionMar 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inactive poly [ADP-ribose] polymerase RCD1
B: Inactive poly [ADP-ribose] polymerase RCD1
E: Inactive poly [ADP-ribose] polymerase RCD1
G: Inactive poly [ADP-ribose] polymerase RCD1
D: Inactive poly [ADP-ribose] polymerase RCD1
F: Inactive poly [ADP-ribose] polymerase RCD1
H: Inactive poly [ADP-ribose] polymerase RCD1
C: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)172,0458
Polymers172,0458
Non-polymers00
Water1,928107
1
A: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
H: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
C: Inactive poly [ADP-ribose] polymerase RCD1


Theoretical massNumber of molelcules
Total (without water)21,5061
Polymers21,5061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.952, 129.952, 468.376
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22E
13A
23G
14A
24D
15A
25F
16A
26H
17A
27C
18B
28E
19B
29G
110B
210D
111B
211F
112B
212H
113B
213C
114E
214G
115E
215D
116E
216F
117E
217H
118E
218C
119G
219D
120G
220F
121G
221H
122G
222C
123D
223F
124D
224H
125D
225C
126F
226H
127F
227C
128H
228C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A273 - 451
2010B273 - 451
1020A273 - 451
2020E273 - 451
1030A273 - 450
2030G273 - 450
1040A273 - 450
2040D273 - 450
1050A273 - 451
2050F273 - 451
1060A273 - 451
2060H273 - 451
1070A273 - 451
2070C273 - 451
1080B273 - 451
2080E273 - 451
1090B273 - 451
2090G273 - 451
10100B273 - 451
20100D273 - 451
10110B273 - 451
20110F273 - 451
10120B273 - 451
20120H273 - 451
10130B273 - 451
20130C273 - 451
10140E273 - 451
20140G273 - 451
10150E273 - 451
20150D273 - 451
10160E273 - 451
20160F273 - 451
10170E273 - 451
20170H273 - 451
10180E273 - 451
20180C273 - 451
10190G273 - 451
20190D273 - 451
10200G273 - 451
20200F273 - 451
10210G273 - 451
20210H273 - 451
10220G273 - 451
20220C273 - 451
10230D273 - 451
20230F273 - 451
10240D273 - 451
20240H273 - 451
10250D273 - 451
20250C273 - 451
10260F273 - 451
20260H273 - 451
10270F273 - 451
20270C273 - 451
10280H272 - 451
20280C272 - 451

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Inactive poly [ADP-ribose] polymerase RCD1 / Protein RADICAL-INDUCED CELL DEATH 1


Mass: 21505.662 Da / Num. of mol.: 8 / Fragment: PARP domain, UNP residues 269-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RCD1, ATP8, CEO1, At1g32230, F3C3.1 / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SoluBL21 / References: UniProt: Q8RY59
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 44.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 1.6M Ammoniumsulfate, 2% PEG1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→156.13 Å / Num. obs: 52927 / % possible obs: 99.7 % / Redundancy: 30.8 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 18.8
Reflection shellResolution: 2.5→2.58 Å / Rmerge(I) obs: 1.019

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Processing

Software
NameVersionClassification
Aimlessdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.22data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→156.13 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / SU B: 22.685 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.754 / ESU R Free: 0.312 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 2684 5.1 %RANDOM
Rwork0.2358 ---
obs0.2371 50228 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 132.93 Å2 / Biso mean: 62.217 Å2 / Biso min: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20.44 Å20 Å2
2--0.88 Å20 Å2
3----2.86 Å2
Refinement stepCycle: final / Resolution: 2.5→156.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10730 0 0 107 10837
Biso mean---51.11 -
Num. residues----1361
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01910938
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210341
X-RAY DIFFRACTIONr_angle_refined_deg1.521.94914737
X-RAY DIFFRACTIONr_angle_other_deg0.999323832
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.16651340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40523.444511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.241151900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9221581
X-RAY DIFFRACTIONr_chiral_restr0.0950.21616
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022357
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A95260.11
12B95260.11
21A104580.1
22E104580.1
31A106700.08
32G106700.08
41A106420.1
42D106420.1
51A92500.11
52F92500.11
61A90940.12
62H90940.12
71A92280.12
72C92280.12
81B93280.12
82E93280.12
91B95720.11
92G95720.11
101B95680.11
102D95680.11
111B98780.08
112F98780.08
121B97420.09
122H97420.09
131B98400.08
132C98400.08
141E105480.1
142G105480.1
151E105080.1
152D105080.1
161E93200.11
162F93200.11
171E91680.12
172H91680.12
181E92500.12
182C92500.12
191G107060.09
192D107060.09
201G93340.11
202F93340.11
211G91820.12
212H91820.12
221G92720.11
222C92720.11
231D93380.1
232F93380.1
241D91760.11
242H91760.11
251D93180.11
252C93180.11
261F97880.08
262H97880.08
271F98600.09
272C98600.09
281H97480.09
282C97480.09
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 197 -
Rwork0.302 3630 -
all-3827 -
obs--99.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.53940.5441-0.1141.9402-0.28064.2919-0.1171-0.1324-0.06130.0640.0944-0.2247-0.45140.04740.02270.10340.04060.02840.04570.01090.056265.186690.9072145.1751
22.4782-0.421-0.51251.48750.66493.52010.0577-0.24350.006-0.1423-0.04970.080.01070.1969-0.00790.07550.0430.03350.06160.01680.034566.65980.7981174.1627
32.29350.1025-0.12091.34270.1734.07090.11550.18770.31720.1912-0.01660.05850.0892-0.5397-0.09890.0571-0.02490.00040.11710.08150.117919.457984.9792223.2142
41.4353-0.27050.65872.02240.44013.89430.093-0.1074-0.0950.0842-0.06660.1150.30830.1868-0.02640.0491-0.01380.02550.0891-0.00740.052946.41648.2348180.8046
51.31220.5202-0.05582.20230.19813.69430.17650.08320.24320.0391-0.09960.3214-0.41580.2598-0.0770.0843-0.01870.07790.1108-0.05680.198546.7039100.8249209.2757
62.02850.1586-0.57041.58-0.07183.42210.0573-0.09480.2679-0.03240.10960.0486-0.29990.035-0.16690.0468-0.02490.0590.031-0.05040.17227.935890.9384252.8652
71.99250.30680.74031.86220.15313.51580.1184-0.0675-0.04550.1659-0.02460.00290.0984-0.3208-0.09390.0247-0.00950.01110.13110.06870.078736.983353.3005210.0726
81.8615-0.1943-0.51592.0384-0.12133.3730.16690.06710.0066-0.1369-0.02820.1022-0.1438-0.3941-0.13870.02890.03080.01620.17210.01630.133437.625895.2799179.9149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A273 - 452
2X-RAY DIFFRACTION2B273 - 451
3X-RAY DIFFRACTION3E273 - 451
4X-RAY DIFFRACTION4G273 - 451
5X-RAY DIFFRACTION5D273 - 451
6X-RAY DIFFRACTION6F273 - 451
7X-RAY DIFFRACTION7H272 - 451
8X-RAY DIFFRACTION8C272 - 451

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