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- PDB-5w3x: Crystal structure of PopP2 in complex with IP6, AcCoA and the WRK... -

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Basic information

Entry
Database: PDB / ID: 5w3x
TitleCrystal structure of PopP2 in complex with IP6, AcCoA and the WRKY domain of RRS1-R .
Components
  • Disease resistance protein RRS1
  • PopP2 protein
KeywordsTRANSCRIPTION / PopP2 / IP6 / YopJ effector / WRKY / RRS-R
Function / homology
Function and homology information


acyltransferase activity / ADP binding / defense response / sequence-specific DNA binding / DNA-binding transcription factor activity / signal transduction / ATP binding / nucleus
Similarity search - Function
WRKY domain / Serine/Threonine acetyltransferase, YopJ / YopJ Serine/Threonine acetyltransferase / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / Leucine-rich repeat 3 / Leucine Rich Repeat ...WRKY domain / Serine/Threonine acetyltransferase, YopJ / YopJ Serine/Threonine acetyltransferase / WRKY domain / WRKY domain superfamily / WRKY DNA -binding domain / WRKY domain profile. / DNA binding domain / Leucine-rich repeat 3 / Leucine Rich Repeat / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain profile. / N-terminal domain of TfIIb / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Single Sheet / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / INOSITOL HEXAKISPHOSPHATE / PopP2 protein / Disease resistance protein RRS1
Similarity search - Component
Biological speciesRalstonia solanacearum (bacteria)
Arabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZhang, Z.M. / Gao, L. / Song, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R35GM119721 United States
CitationJournal: Nat Plants / Year: 2017
Title: Mechanism of host substrate acetylation by a YopJ family effector.
Authors: Zhang, Z.M. / Ma, K.W. / Gao, L. / Hu, Z. / Schwizer, S. / Ma, W. / Song, J.
History
DepositionJun 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 14, 2020Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PopP2 protein
B: Disease resistance protein RRS1
C: PopP2 protein
D: Disease resistance protein RRS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,15511
Polymers95,9924
Non-polymers3,1627
Water9,170509
1
A: PopP2 protein
B: Disease resistance protein RRS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5315
Polymers47,9962
Non-polymers1,5353
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-26 kcal/mol
Surface area17630 Å2
MethodPISA
2
C: PopP2 protein
D: Disease resistance protein RRS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6236
Polymers47,9962
Non-polymers1,6274
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-26 kcal/mol
Surface area17980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.539, 87.542, 87.548
Angle α, β, γ (deg.)71.54, 84.04, 84.00
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein PopP2 protein


Mass: 38701.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia solanacearum (bacteria) / Gene: popp, RUN1985_v1_1190012 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0S4VB05
#2: Protein Disease resistance protein RRS1 / / Disease resistance protein RCH2 / Probable WRKY transcription factor 52 / Resistance to ...Disease resistance protein RCH2 / Probable WRKY transcription factor 52 / Resistance to Colletotrichum higginsianum 2 protein / Resistance to Ralstonia solanacearum 1 protein


Mass: 9294.553 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RRS1, RCH2, RRS1-R, WRKY52 / Production host: Escherichia coli (E. coli) / References: UniProt: C4B7M5

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Non-polymers , 5 types, 516 molecules

#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE / Phytic acid


Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H18O24P6
#4: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25 mM Tris-HCl (pH 7.5), 250 mM NaCl, 50 mM Arg/Glu, 5% glycerol and 2 mM IP6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.91→82.81 Å / Num. obs: 80778 / % possible obs: 91.8 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.4
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 1.5 % / Rmerge(I) obs: 1.641 / Mean I/σ(I) obs: 0.5 / Num. unique obs: 90528 / % possible all: 63.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Cootmodel building
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W3T
Resolution: 2→82.809 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2118 1781 2.2 %
Rwork0.1831 --
obs0.1837 80778 93.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→82.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6270 0 142 509 6921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086518
X-RAY DIFFRACTIONf_angle_d1.258857
X-RAY DIFFRACTIONf_dihedral_angle_d14.6752393
X-RAY DIFFRACTIONf_chiral_restr0.055986
X-RAY DIFFRACTIONf_plane_restr0.0061148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.05410.36251340.31286121X-RAY DIFFRACTION95
2.0541-2.11450.33931360.27666108X-RAY DIFFRACTION95
2.1145-2.18280.30121380.24496176X-RAY DIFFRACTION95
2.1828-2.26080.29471390.22416036X-RAY DIFFRACTION94
2.2608-2.35130.22621380.20615991X-RAY DIFFRACTION93
2.3513-2.45840.23271370.19566142X-RAY DIFFRACTION95
2.4584-2.5880.21321400.19076135X-RAY DIFFRACTION95
2.588-2.75010.19531380.18686062X-RAY DIFFRACTION94
2.7501-2.96250.2961370.1986023X-RAY DIFFRACTION93
2.9625-3.26060.25561440.19016203X-RAY DIFFRACTION95
3.2606-3.73240.17231310.17435922X-RAY DIFFRACTION92
3.7324-4.70240.15841320.14246138X-RAY DIFFRACTION95
4.7024-82.87970.16961370.15655940X-RAY DIFFRACTION92
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.2177-0.01680.03210.0086-0.10640.2132-0.0358-0.2852-0.15880.0234-0.043-0.06390.03390.0994-00.27710.01980.01330.28650.04120.2813-36.571136.8305-66.0599
20.9823-0.3001-0.04770.6058-0.25980.38590.01610.05960.1187-0.0325-0.0188-0.02680.0151-0.0042-00.2411-0.0049-0.00720.2016-0.00180.2646-34.489553.293-82.5582
30.1516-0.05230.06320.4771-0.13830.43250.0071-0.1707-0.1356-0.0003-0.0002-0.00990.02750.0471-00.28180.0212-0.00140.26090.01440.2748-33.640339.3394-71.3581
40.0099-0.01370.00740.0128-0.00680.0059-0.37270.0003-0.0819-0.2037-0.3087-0.0381-0.2361-0.04760.00010.81550.17720.04020.5942-0.03030.562-38.222335.8049-108.3132
50.0243-0.0227-0.02450.01960.02420.02240.0046-0.07090.09120.0196-0.0076-0.03830.0180.1808-0.00020.3991-0.0025-0.03110.2798-0.02240.3174-37.355242.6636-96.6055
60.0073-0.0055-0.00570.00520.00690.00810.06620.091-0.0656-0.02750.0320.0360.10350.00170.00010.3940.0032-0.05960.3213-0.04030.3803-29.150231.0895-88.7361
70.02950.03830.02810.05980.07040.0813-0.03590.1512-0.0005-0.06130.00070.1847-0.04190.012-0.00010.41060.0658-0.12130.3604-0.08650.3826-42.655641.2172-99.3501
80.004-0.0022-0.00290.0029-0.0060.0390.13170.03-0.03620.0298-0.03650.0420.0080.03170.00010.86590.2313-0.37550.8495-0.20021.4239-28.599523.9941-95.9977
90.0145-0.01510.00570.0151-0.00560.0087-0.04280.00090.0162-0.11940.21920.25960.0164-0.0792-0.00020.56580.0955-0.13130.4231-0.14920.4872-40.575731.2995-99.759
100.0060.0020.00630.0028-0.00180.01010.07670.0112-0.1182-0.1088-0.18210.1252-0.0182-0.10250.00030.8319-0.0042-0.41620.68320.09430.7576-49.615840.7393-108.6326
110.0106-0.0533-0.00370.04720.00860.1918-0.0847-0.1252-0.1665-0.02640.07690.05530.0573-0.010200.30870.00870.02810.31380.08280.3494-30.204269.3139-97.7968
120.07160.0135-0.02740.0927-0.13170.124-0.0183-0.1818-0.13390.12950.0351-0.01070.1191-0.11-00.2977-0.00320.00780.3474-0.00390.2381-37.205880.3892-103.1221
130.7317-0.1448-0.29940.3869-0.08120.76490.0060.12650.05120.016-0.0058-0.0104-0.03360.024800.2536-0.00950.00170.282-0.01250.2269-32.596688.4301-122.6223
140.4639-0.0454-0.14690.00970.01920.1567-0.03030.096-0.08610.03680.07130.0631-0.04870.008600.269-0.0191-0.00540.3333-0.02260.302-53.268181.1043-117.7321
150.087-0.03410.05470.3073-0.06620.6171-0.0487-0.1461-0.1290.09380.00880.039-0.0117-0.042200.2540.01030.00610.26710.01560.2373-37.714880.1905-104.5367
160.1156-0.06650.00490.05960.01230.010.0570.0071-0.00190.04980.03130.06610.01370.06460.12480.7232-0.05430.04270.332-0.51320.6988-32.2396113.959-102.1505
170.00390.0021-0.00260.01860.01470.0091-0.068-0.14420.1045-0.0289-0.0573-0.1692-0.0741-0.12760.00020.897-0.08550.21830.6644-0.12740.6261-33.6952116.4926-112.082
180.0299-0.0169-0.01360.03240.0260.01960.13330.0593-0.0426-0.00690.04310.21190.01580.00170.00040.3897-0.03510.02260.234-0.00860.2756-34.3923103.4196-115.6989
190.03380.00360.04020.03060.01250.03770.0375-0.08290.1834-0.07620.07420.0438-0.12050.00860.00020.4664-0.05010.03930.3566-0.04790.3975-37.8547101.7753-107.494
200.0213-0.01120.00030.07540.04750.0319-0.1083-0.03350.1752-0.11250.026-0.13350.01870.1847-0.00010.5246-0.13280.08270.4676-0.0690.4935-27.6118107.3597-116.1013
210.00590.004-0.00650.0223-0.0090.00770.19370.00550.05820.02030.09040.00360.0242-0.0064-0.00020.7884-0.18240.32821.2206-0.24951.0311-43.099108.4663-97.5793
220.00080.0029-0.00140.0082-0.00560.0043-0.1420.05330.026-0.0277-0.04160.0184-0.06750.2837-0.00060.6304-0.11240.16640.4674-0.18040.5043-31.2216109.8858-105.8897
230.0089-0.0011-0.0070.0049-0.00060.00360.0368-0.1630.0094-0.08320.1038-0.0397-0.04460.0945-00.8793-0.34490.18260.795-0.08580.7306-21.9867115.2062-117.589
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 152 through 208 )
2X-RAY DIFFRACTION2chain 'A' and (resid 209 through 427 )
3X-RAY DIFFRACTION3chain 'A' and (resid 428 through 486 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1207 through 1214 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1215 through 1221 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1222 through 1229 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1230 through 1251 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1252 through 1258 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1259 through 1264 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1265 through 1273 )
11X-RAY DIFFRACTION11chain 'C' and (resid 145 through 178 )
12X-RAY DIFFRACTION12chain 'C' and (resid 179 through 208 )
13X-RAY DIFFRACTION13chain 'C' and (resid 209 through 378 )
14X-RAY DIFFRACTION14chain 'C' and (resid 379 through 427 )
15X-RAY DIFFRACTION15chain 'C' and (resid 428 through 487 )
16X-RAY DIFFRACTION16chain 'D' and (resid 1197 through 1201 )
17X-RAY DIFFRACTION17chain 'D' and (resid 1202 through 1214 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1215 through 1221 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1222 through 1235 )
20X-RAY DIFFRACTION20chain 'D' and (resid 1236 through 1251 )
21X-RAY DIFFRACTION21chain 'D' and (resid 1252 through 1258 )
22X-RAY DIFFRACTION22chain 'D' and (resid 1259 through 1264 )
23X-RAY DIFFRACTION23chain 'D' and (resid 1265 through 1273 )

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