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- PDB-7plq: Crystal structure of the PARP domain of wheat SRO1 -

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Basic information

Entry
Database: PDB / ID: 7plq
TitleCrystal structure of the PARP domain of wheat SRO1
ComponentsSIMILAR TO RCD1 (SRO1)
KeywordsPLANT PROTEIN / poly(ADP-ribose)-polymerase (PARP) domain
Function / homology
Function and homology information


response to stress / NAD+ poly-ADP-ribosyltransferase activity
Similarity search - Function
Inactive poly [ADP-ribose] polymerase RCD1/SRO1-5 / RST domain / RCD1-SRO-TAF4 (RST) plant domain / RST domain profile. / Poly(ADP-ribose) polymerase, catalytic domain / PARP catalytic domain profile.
Similarity search - Domain/homology
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE / PARP catalytic domain-containing protein
Similarity search - Component
Biological speciesTriticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.13 Å
AuthorsWirthmueller, L. / Loll, B.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)WI 3670/2-1 Germany
Citation
Journal: Plant Cell / Year: 2022
Title: The superior salinity tolerance of bread wheat cultivar Shanrong No. 3 is unlikely to be caused by elevated Ta-sro1 poly-(ADP-ribose) polymerase activity.
Authors: Vogt, S. / Feijs, K. / Hosch, S. / De Masi, R. / Lintermann, R. / Loll, B. / Wirthmueller, L.
#1: Journal: Biorxiv / Year: 2021
Title: The superior salinity tolerance of wheat cultivar Shanrong No. 3 cannot be attributed to elevated Ta-sro1 poly(ADP-ribose) polymerase activity
Authors: Vogt, S. / Feijs, K. / Hosch, S. / Lintermann, R. / Loll, B. / Wirthmueller, L.
History
DepositionSep 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Nov 9, 2022Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SIMILAR TO RCD1 (SRO1)
B: SIMILAR TO RCD1 (SRO1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4508
Polymers43,8792
Non-polymers5716
Water1,49583
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A: SIMILAR TO RCD1 (SRO1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1283
Polymers21,9401
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SIMILAR TO RCD1 (SRO1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3225
Polymers21,9401
Non-polymers3824
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.513, 34.373, 132.581
Angle α, β, γ (deg.)90.000, 101.220, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 250 through 261 or resid 263...
21(chain B and (resid 250 through 261 or resid 263...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLYGLY(chain A and (resid 250 through 261 or resid 263...AA250 - 2617 - 18
12GLYGLYTYRTYR(chain A and (resid 250 through 261 or resid 263...AA263 - 27520 - 32
13THRTHRGLNGLN(chain A and (resid 250 through 261 or resid 263...AA277 - 29234 - 49
14GLUGLULYSLYS(chain A and (resid 250 through 261 or resid 263...AA294 - 29951 - 56
15HISHISLYSLYS(chain A and (resid 250 through 261 or resid 263...AA301 - 31658 - 73
16THRTHRLYSLYS(chain A and (resid 250 through 261 or resid 263...AA318 - 33275 - 89
17VALVALTYRTYR(chain A and (resid 250 through 261 or resid 263...AA338 - 35795 - 114
18ASPASPLEULEU(chain A and (resid 250 through 261 or resid 263...AA359 - 402116 - 159
19PROPROASNASN(chain A and (resid 250 through 261 or resid 263...AA405 - 414162 - 171
110HISHISHISHIS(chain A and (resid 250 through 261 or resid 263...AA416173
111HISHISALAALA(chain A and (resid 250 through 261 or resid 263...AA418 - 429175 - 186
21VALVALGLYGLY(chain B and (resid 250 through 261 or resid 263...BB250 - 2617 - 18
22GLYGLYTYRTYR(chain B and (resid 250 through 261 or resid 263...BB263 - 27520 - 32
23THRTHRGLNGLN(chain B and (resid 250 through 261 or resid 263...BB277 - 29234 - 49
24GLUGLULYSLYS(chain B and (resid 250 through 261 or resid 263...BB294 - 29951 - 56
25HISHISLYSLYS(chain B and (resid 250 through 261 or resid 263...BB301 - 31658 - 73
26THRTHRLYSLYS(chain B and (resid 250 through 261 or resid 263...BB318 - 33275 - 89
27VALVALTYRTYR(chain B and (resid 250 through 261 or resid 263...BB338 - 35795 - 114
28ASPASPLEULEU(chain B and (resid 250 through 261 or resid 263...BB359 - 402116 - 159
29PROPROASNASN(chain B and (resid 250 through 261 or resid 263...BB405 - 414162 - 171
210HISHISHISHIS(chain B and (resid 250 through 261 or resid 263...BB416173
211HISHISALAALA(chain B and (resid 250 through 261 or resid 263...BB418 - 429175 - 186

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SIMILAR TO RCD1 (SRO1)


Mass: 21939.543 Da / Num. of mol.: 2 / Fragment: PARP domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Triticum aestivum (bread wheat) / Plasmid: pOPIN-F / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle / References: UniProt: A0A3B6LXD6

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Non-polymers , 5 types, 89 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.05 Å3/Da / Density % sol: 39.93 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.8
Details: 0.1 MES, 0.2 M ammonium sulfate, 17% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.13→43.35 Å / Num. obs: 37083 / % possible obs: 97.3 % / Redundancy: 6.97 % / Biso Wilson estimate: 40.39 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.0194 / Net I/σ(I): 8.69
Reflection shellResolution: 2.13→2.26 Å / Redundancy: 6.28 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5558 / CC1/2: 0.416 / Rrim(I) all: 0.1664 / % possible all: 89.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.13→43.35 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 973 5 %
Rwork0.2141 18479 -
obs0.2167 19452 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 186.38 Å2 / Biso mean: 52.1544 Å2 / Biso min: 22.54 Å2
Refinement stepCycle: final / Resolution: 2.13→43.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2846 0 33 83 2962
Biso mean--55.02 43.51 -
Num. residues----361
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1404X-RAY DIFFRACTION7.875TORSIONAL
12B1404X-RAY DIFFRACTION7.875TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.13-2.240.34981270.2962417254490
2.24-2.380.34921400.27972653279399
2.38-2.570.31151390.248226372776100
2.57-2.820.28871420.21712694283699
2.82-3.230.25231370.20072613275097
3.23-4.070.25761420.18632686282899
4.07-43.350.23631460.21022779292598
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)
11.0461-0.41420.21251.22110.51015.0774-0.0150.06050.01760.03490.0409-0.0015-0.083-0.2078-0.03130.3705-0.00230.04240.29620.0220.29643.52859.09747.6343
21.8827-0.1656-1.96211.84590.52434.8601-0.0106-0.0479-0.01550.04690.0190.2164-0.0081-0.4315-0.00430.3310.0199-0.0280.28440.03450.31049.82385.897214.9182
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 250 through 431)A250 - 431
2X-RAY DIFFRACTION2(chain 'B' and resid 247 through 429)B247 - 429

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