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

ID or keywords:

Entry

Database: PDB / ID: 5w3x

Title

Crystal structure of PopP2 in complex with IP6, AcCoA and the WRKY domain of RRS1-R .

Components

Disease resistance protein RRS1
PopP2 protein

Keywords

TRANSCRIPTION / PopP2 / IP6 / YopJ effector / WRKY / RRS-R

Function / homology

Function and homology information

acyltransferase activity / defense response / ADP binding / sequence-specific DNA binding / DNA-binding transcription factor activity / signal transduction / ATP binding / nucleus
Similarity search - Function

Biological species

Ralstonia solanacearum (bacteria)

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Zhang, Z.M. / Gao, L. / Song, J.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Jun 8, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 9, 2017	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 14, 2020	Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.4	Oct 4, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5w3x.cif.gz	342.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5w3x.ent.gz	276.6 KB	Display	PDB format
PDBx/mmJSON format	5w3x.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5w3x_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	5w3x_full_validation.pdf.gz	2.3 MB	Display
Data in XML	5w3x_validation.xml.gz	38.6 KB	Display
Data in CIF	5w3x_validation.cif.gz	55.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w3/5w3x ftp://data.pdbj.org/pub/pdb/validation_reports/w3/5w3x	HTTPS FTP

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Related structure data

Related structure data	5w3tSC 5w3yC 5w40C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6tyr-d 6s21-2 6hsw-1 6ftw-1 6mz0-2 6s21-3 2x87-d 6hsw-2 6s21-1 1yey-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#177 - Sep 2014 Apoptosomes similarity (3) #143 - Nov 2011 Toll-like Receptors similarity (3) #110 - Feb 2009 Auxin and TIR1 Ubiquitin Ligase similarity (1) #225 - Sep 2018 Phytase similarity (1) #218 - Feb 2018 EPSP Synthase and Weedkillers similarity (1) #88 - Apr 2007 Clathrin similarity (1)

Deposited unit

A: PopP2 protein

B: Disease resistance protein RRS1

C: PopP2 protein

D: Disease resistance protein RRS1

hetero molecules

99.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: PopP2 protein

B: Disease resistance protein RRS1

hetero molecules

defined by author&software
Evidence: gel filtration
49.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PopP2 protein

D: Disease resistance protein RRS1

hetero molecules

defined by author&software
49.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	1
Space group name H-M	P1

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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

#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 ...

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 Mass: 660.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₈O₂₄P₆
#4: Chemical	ChemComp-ACO / ACETYL COENZYME A 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 Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.53 Å³/Da / Density % sol: 65.2 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.98 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.91→82.81 Å / Num. obs: 80778 / % possible obs: 91.8 % / Redundancy: 2.7 % / R_merge(I) obs: 0.077 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.91→1.94 Å / Redundancy: 1.5 % / R_merge(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

Name	Version	Classification
PHENIX	1.9_1692	refinement
Coot		model building
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5W3T

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

	R_factor	Num. reflection	% reflection
R_free	0.2118	1781	2.2 %
R_work	0.1831	-	-
obs	0.1837	80778	93.97 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2→82.809 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6270	0	142	509	6921

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	6518
X-RAY DIFFRACTION	f_angle_d	1.25	8857
X-RAY DIFFRACTION	f_dihedral_angle_d	14.675	2393
X-RAY DIFFRACTION	f_chiral_restr	0.055	986
X-RAY DIFFRACTION	f_plane_restr	0.006	1148

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.0541	0.3625	134	0.3128	6121	X-RAY DIFFRACTION	95
2.0541-2.1145	0.3393	136	0.2766	6108	X-RAY DIFFRACTION	95
2.1145-2.1828	0.3012	138	0.2449	6176	X-RAY DIFFRACTION	95
2.1828-2.2608	0.2947	139	0.2241	6036	X-RAY DIFFRACTION	94
2.2608-2.3513	0.2262	138	0.2061	5991	X-RAY DIFFRACTION	93
2.3513-2.4584	0.2327	137	0.1956	6142	X-RAY DIFFRACTION	95
2.4584-2.588	0.2132	140	0.1907	6135	X-RAY DIFFRACTION	95
2.588-2.7501	0.1953	138	0.1868	6062	X-RAY DIFFRACTION	94
2.7501-2.9625	0.296	137	0.198	6023	X-RAY DIFFRACTION	93
2.9625-3.2606	0.2556	144	0.1901	6203	X-RAY DIFFRACTION	95
3.2606-3.7324	0.1723	131	0.1743	5922	X-RAY DIFFRACTION	92
3.7324-4.7024	0.1584	132	0.1424	6138	X-RAY DIFFRACTION	95
4.7024-82.8797	0.1696	137	0.1565	5940	X-RAY DIFFRACTION	92

Refinement TLS params.

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

ID	L11 (°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)
1	0.2177	-0.0168	0.0321	0.0086	-0.1064	0.2132	-0.0358	-0.2852	-0.1588	0.0234	-0.043	-0.0639	0.0339	0.0994	-0	0.2771	0.0198	0.0133	0.2865	0.0412	0.2813	-36.5711	36.8305	-66.0599
2	0.9823	-0.3001	-0.0477	0.6058	-0.2598	0.3859	0.0161	0.0596	0.1187	-0.0325	-0.0188	-0.0268	0.0151	-0.0042	-0	0.2411	-0.0049	-0.0072	0.2016	-0.0018	0.2646	-34.4895	53.293	-82.5582
3	0.1516	-0.0523	0.0632	0.4771	-0.1383	0.4325	0.0071	-0.1707	-0.1356	-0.0003	-0.0002	-0.0099	0.0275	0.0471	-0	0.2818	0.0212	-0.0014	0.2609	0.0144	0.2748	-33.6403	39.3394	-71.3581
4	0.0099	-0.0137	0.0074	0.0128	-0.0068	0.0059	-0.3727	0.0003	-0.0819	-0.2037	-0.3087	-0.0381	-0.2361	-0.0476	0.0001	0.8155	0.1772	0.0402	0.5942	-0.0303	0.562	-38.2223	35.8049	-108.3132
5	0.0243	-0.0227	-0.0245	0.0196	0.0242	0.0224	0.0046	-0.0709	0.0912	0.0196	-0.0076	-0.0383	0.018	0.1808	-0.0002	0.3991	-0.0025	-0.0311	0.2798	-0.0224	0.3174	-37.3552	42.6636	-96.6055
6	0.0073	-0.0055	-0.0057	0.0052	0.0069	0.0081	0.0662	0.091	-0.0656	-0.0275	0.032	0.036	0.1035	0.0017	0.0001	0.394	0.0032	-0.0596	0.3213	-0.0403	0.3803	-29.1502	31.0895	-88.7361
7	0.0295	0.0383	0.0281	0.0598	0.0704	0.0813	-0.0359	0.1512	-0.0005	-0.0613	0.0007	0.1847	-0.0419	0.012	-0.0001	0.4106	0.0658	-0.1213	0.3604	-0.0865	0.3826	-42.6556	41.2172	-99.3501
8	0.004	-0.0022	-0.0029	0.0029	-0.006	0.039	0.1317	0.03	-0.0362	0.0298	-0.0365	0.042	0.008	0.0317	0.0001	0.8659	0.2313	-0.3755	0.8495	-0.2002	1.4239	-28.5995	23.9941	-95.9977
9	0.0145	-0.0151	0.0057	0.0151	-0.0056	0.0087	-0.0428	0.0009	0.0162	-0.1194	0.2192	0.2596	0.0164	-0.0792	-0.0002	0.5658	0.0955	-0.1313	0.4231	-0.1492	0.4872	-40.5757	31.2995	-99.759
10	0.006	0.002	0.0063	0.0028	-0.0018	0.0101	0.0767	0.0112	-0.1182	-0.1088	-0.1821	0.1252	-0.0182	-0.1025	0.0003	0.8319	-0.0042	-0.4162	0.6832	0.0943	0.7576	-49.6158	40.7393	-108.6326
11	0.0106	-0.0533	-0.0037	0.0472	0.0086	0.1918	-0.0847	-0.1252	-0.1665	-0.0264	0.0769	0.0553	0.0573	-0.0102	0	0.3087	0.0087	0.0281	0.3138	0.0828	0.3494	-30.2042	69.3139	-97.7968
12	0.0716	0.0135	-0.0274	0.0927	-0.1317	0.124	-0.0183	-0.1818	-0.1339	0.1295	0.0351	-0.0107	0.1191	-0.11	-0	0.2977	-0.0032	0.0078	0.3474	-0.0039	0.2381	-37.2058	80.3892	-103.1221
13	0.7317	-0.1448	-0.2994	0.3869	-0.0812	0.7649	0.006	0.1265	0.0512	0.016	-0.0058	-0.0104	-0.0336	0.0248	0	0.2536	-0.0095	0.0017	0.282	-0.0125	0.2269	-32.5966	88.4301	-122.6223
14	0.4639	-0.0454	-0.1469	0.0097	0.0192	0.1567	-0.0303	0.096	-0.0861	0.0368	0.0713	0.0631	-0.0487	0.0086	0	0.269	-0.0191	-0.0054	0.3333	-0.0226	0.302	-53.2681	81.1043	-117.7321
15	0.087	-0.0341	0.0547	0.3073	-0.0662	0.6171	-0.0487	-0.1461	-0.129	0.0938	0.0088	0.039	-0.0117	-0.0422	0	0.254	0.0103	0.0061	0.2671	0.0156	0.2373	-37.7148	80.1905	-104.5367
16	0.1156	-0.0665	0.0049	0.0596	0.0123	0.01	0.057	0.0071	-0.0019	0.0498	0.0313	0.0661	0.0137	0.0646	0.1248	0.7232	-0.0543	0.0427	0.332	-0.5132	0.6988	-32.2396	113.959	-102.1505
17	0.0039	0.0021	-0.0026	0.0186	0.0147	0.0091	-0.068	-0.1442	0.1045	-0.0289	-0.0573	-0.1692	-0.0741	-0.1276	0.0002	0.897	-0.0855	0.2183	0.6644	-0.1274	0.6261	-33.6952	116.4926	-112.082
18	0.0299	-0.0169	-0.0136	0.0324	0.026	0.0196	0.1333	0.0593	-0.0426	-0.0069	0.0431	0.2119	0.0158	0.0017	0.0004	0.3897	-0.0351	0.0226	0.234	-0.0086	0.2756	-34.3923	103.4196	-115.6989
19	0.0338	0.0036	0.0402	0.0306	0.0125	0.0377	0.0375	-0.0829	0.1834	-0.0762	0.0742	0.0438	-0.1205	0.0086	0.0002	0.4664	-0.0501	0.0393	0.3566	-0.0479	0.3975	-37.8547	101.7753	-107.494
20	0.0213	-0.0112	0.0003	0.0754	0.0475	0.0319	-0.1083	-0.0335	0.1752	-0.1125	0.026	-0.1335	0.0187	0.1847	-0.0001	0.5246	-0.1328	0.0827	0.4676	-0.069	0.4935	-27.6118	107.3597	-116.1013
21	0.0059	0.004	-0.0065	0.0223	-0.009	0.0077	0.1937	0.0055	0.0582	0.0203	0.0904	0.0036	0.0242	-0.0064	-0.0002	0.7884	-0.1824	0.3282	1.2206	-0.2495	1.0311	-43.099	108.4663	-97.5793
22	0.0008	0.0029	-0.0014	0.0082	-0.0056	0.0043	-0.142	0.0533	0.026	-0.0277	-0.0416	0.0184	-0.0675	0.2837	-0.0006	0.6304	-0.1124	0.1664	0.4674	-0.1804	0.5043	-31.2216	109.8858	-105.8897
23	0.0089	-0.0011	-0.007	0.0049	-0.0006	0.0036	0.0368	-0.163	0.0094	-0.0832	0.1038	-0.0397	-0.0446	0.0945	-0	0.8793	-0.3449	0.1826	0.795	-0.0858	0.7306	-21.9867	115.2062	-117.589

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 152 through 208 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 209 through 427 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 428 through 486 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 1207 through 1214 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 1215 through 1221 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 1222 through 1229 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1230 through 1251 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1252 through 1258 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1259 through 1264 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 1265 through 1273 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 145 through 178 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 179 through 208 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 209 through 378 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 379 through 427 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 428 through 487 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1197 through 1201 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 1202 through 1214 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 1215 through 1221 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1222 through 1235 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1236 through 1251 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 1252 through 1258 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 1259 through 1264 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 1265 through 1273 )

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Protein , 2 types, 4 molecules ACBD

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Non-polymers , 5 types, 516 molecules

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