PDB-5w3t: Crystal structure of PopP2 in complex with IP6

ID or keywords:

Entry

Database: PDB / ID: 5w3t

Title

Crystal structure of PopP2 in complex with IP6

Components

PopP2 protein

Keywords

TRANSCRIPTION / YopJ effector / PopP2 / IP6

Function / homology

Serine/Threonine acetyltransferase, YopJ / YopJ Serine/Threonine acetyltransferase / acyltransferase activity / INOSITOL HEXAKISPHOSPHATE / PopP2 protein

Function and homology information

Biological species

Ralstonia solanacearum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.15 Å

Authors

Song, J. / Zhang, Z.M.

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	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5w3t.cif.gz	524.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5w3t.ent.gz	434.3 KB	Display	PDB format
PDBx/mmJSON format	5w3t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5w3t_validation.pdf.gz	3.3 MB	Display	wwPDB validaton report
Full document	5w3t_full_validation.pdf.gz	3.3 MB	Display
Data in XML	5w3t_validation.xml.gz	52.6 KB	Display
Data in CIF	5w3t_validation.cif.gz	72.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w3/5w3t ftp://data.pdbj.org/pub/pdb/validation_reports/w3/5w3t	HTTPS FTP

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Related structure data

Related structure data	5w3xC 5w3yC 5w40C C: citing same article (ref.)
Similar structure data	5w3y-2 5ec6-d 5w40-1 5w40-4 2gp3-2 3v94-3 4ncp-3 5w3y-1 2a8u-d 4hon-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

Related structure data

5w3xC

5w3yC

5w40C

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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: PopP2 protein

C: PopP2 protein

D: PopP2 protein

hetero molecules

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

1

A: PopP2 protein

hetero molecules

defined by author&software
Evidence: gel filtration
39.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PopP2 protein

hetero molecules

defined by author&software
39.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: PopP2 protein

hetero molecules

defined by author&software
39.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: PopP2 protein

hetero molecules

defined by author&software
39.4 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	77.987, 78.956, 79.902
Angle α, β, γ (deg.)	103.36, 112.12, 111.54
Int Tables number	1
Space group name H-M	P1

#1: Protein	PopP2 protein Mass: 38698.660 Da / Num. of mol.: 4 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: Chemical	ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE Mass: 660.035 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₈O₂₄P₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.47 Å³/Da / Density % sol: 50.29 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 20% (v/v) PEG4000 and 10% (v/v) glycerol

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9774 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: 0.9774 Å / Relative weight: 1
Reflection	Resolution: 2.06→66.87 Å / Num. obs: 75480 / % possible obs: 93.6 % / Redundancy: 2.6 % / R_merge(I) obs: 0.066 / Net I/σ(I): 10.1
Reflection shell	Resolution: 2.06→2.1 Å / Redundancy: 2.6 % / R_merge(I) obs: 1.159 / Mean I/σ(I) obs: 0.8 / % possible all: 94.1

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.15→66.349 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.48

	R_factor	Num. reflection	% reflection
R_free	0.2427	1856	2.46 %
R_work	0.1885	-	-
obs	0.1897	75480	93.55 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.15→66.349 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9974	0	156	390	10520

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	10287
X-RAY DIFFRACTION	f_angle_d	0.969	13982
X-RAY DIFFRACTION	f_dihedral_angle_d	11.904	3780
X-RAY DIFFRACTION	f_chiral_restr	0.046	1609
X-RAY DIFFRACTION	f_plane_restr	0.005	1835

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 (%)
2.15-2.2081	0.3425	143	0.3028	5654	X-RAY DIFFRACTION	94
2.2081-2.2731	0.3364	137	0.2934	5616	X-RAY DIFFRACTION	93
2.2731-2.3465	0.3553	155	0.2719	5559	X-RAY DIFFRACTION	92
2.3465-2.4304	0.3218	141	0.2621	5734	X-RAY DIFFRACTION	95
2.4304-2.5277	0.2835	148	0.2426	5741	X-RAY DIFFRACTION	94
2.5277-2.6427	0.2606	136	0.2181	5676	X-RAY DIFFRACTION	94
2.6427-2.7821	0.2517	143	0.2098	5641	X-RAY DIFFRACTION	93
2.7821-2.9564	0.2382	147	0.2034	5604	X-RAY DIFFRACTION	93
2.9564-3.1846	0.2407	139	0.1986	5788	X-RAY DIFFRACTION	95
3.1846-3.5051	0.2602	148	0.1879	5681	X-RAY DIFFRACTION	94
3.5051-4.0122	0.1971	148	0.1646	5590	X-RAY DIFFRACTION	92
4.0122-5.0547	0.2033	144	0.149	5697	X-RAY DIFFRACTION	94
5.0547-66.3801	0.2365	127	0.1641	5643	X-RAY DIFFRACTION	93

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	4.4294	2.5451	-0.8564	4.2031	-1.5237	2.5588	-0.5708	0.5858	-0.3689	-0.9033	0.4257	-0.2104	0.5682	-0.5152	-0.0079	0.5272	-0.1074	-0.0083	0.3651	-0.0671	0.3734	36.967	20.0167	16.8894
2	2.8838	1.1222	-1.7491	2.7385	1.4193	3.991	0.0031	-0.0111	0.4275	-0.1735	-0.1358	0.6743	-0.045	-0.7493	0.0864	0.2867	0.0033	-0.0594	0.5325	-0.01	0.5388	23.7728	29.7389	32.0721
3	2.9531	0.642	-1.9323	2.4542	0.8707	3.7028	0.0866	-0.1808	0.5053	0.0335	-0.16	0.2949	-0.4157	-0.4989	0.029	0.3344	0.0708	-0.0574	0.4741	-0.0432	0.4342	31.4492	38.1299	39.5685
4	3.0344	0.096	-0.2792	3.3906	2.0085	7.0989	-0.1449	0.0473	0.2407	-0.2472	-0.0192	-0.0618	-0.5159	-0.0551	0.1423	0.2909	-0.0452	-0.0469	0.2623	-0.0068	0.4103	50.7438	36.3678	31.5465
5	2.9564	1.8876	0.3958	5.7982	-0.1294	1.6741	-0.1431	0.0173	-0.0726	-0.4603	0.1558	0.4227	0.3737	-0.4569	-0.0003	0.4806	-0.1031	-0.0317	0.4074	-0.0043	0.2925	34.1143	17.9751	20.8173
6	7.0283	3.7636	0.483	2.993	0.4321	2.7189	-0.0469	0.0165	-0.1216	-0.1165	0.2856	-1.1196	-0.5283	0.3612	-0.2449	0.4063	-0.0105	0.0086	0.4947	-0.0567	0.4358	82.7827	2.5773	-8.1116
7	2.2586	2.0726	0.3132	6.6495	2.6631	1.6809	0.2065	-0.1054	-0.445	0.7328	0.2368	-0.2853	0.364	0.061	-0.3861	0.4112	-0.005	-0.0583	0.4409	0.0134	0.3305	71.7488	-6.1982	-2.0291
8	5.3485	-0.5118	-0.4562	2.6839	0.8751	2.6395	0.1948	-1.1399	0.4433	0.4804	-0.144	-0.17	-0.2061	-0.1134	-0.0243	0.5382	-0.0256	0.0346	0.6751	-0.1067	0.3543	63.5163	6.4882	9.0325
9	3.8084	-0.8639	-0.6632	2.5581	1.6327	3.4256	-0.041	-0.7826	0.1195	0.4913	-0.0044	0.2769	-0.0752	-0.7102	0.0232	0.4895	0.0538	0.0438	0.7867	0.0074	0.3512	49.9928	2.575	5.719
10	6.0302	-1.4806	0.0103	5.2121	0.3685	2.77	0.05	-0.3954	-0.35	0.2098	0.0096	0.0299	0.2004	-0.239	-0.0811	0.2637	-0.0808	-0.0482	0.3688	0.0397	0.2281	53.8461	-11.718	-9.8003
11	5.3063	2.9767	0.7321	4.4219	-0.7349	2.8887	-0.0284	-0.0154	0.0893	0.1201	-0.0133	-0.2526	-0.3616	0.0547	0.0316	0.3131	0.0223	-0.0169	0.3309	-0.0184	0.3248	75.5084	3.3369	-4.3409
12	8.0207	-3.5084	5.7884	5.4512	-4.7942	8.7582	0.402	0.9607	0.2599	-0.5751	-0.2981	0.4333	0.0145	0.3391	-0.0201	0.568	0.015	0.0512	0.5012	0.0044	0.3872	48.5225	22.2264	-54.3362
13	2.9779	-3.719	1.2006	4.5038	-1.5714	1.9792	-0.0264	0.1622	0.7839	0.1807	-0.2795	-0.8301	-0.3654	0.2503	0.3175	0.451	-0.0401	-0.053	0.3813	-0.0031	0.4104	52.9365	21.5791	-38.8951
14	7.8379	1.2188	0.575	4.2844	0.5674	5.3431	0.1086	-0.4421	1.1872	0.8025	-0.155	-0.1009	-1.055	-0.0505	-0.0114	0.728	0.0647	-0.1133	0.3608	-0.0766	0.4727	42.668	33.0505	-33.2663
15	4.6835	-1.4399	-0.7779	3.988	-0.4161	2.8237	0.0901	0.2954	0.5483	0.0856	0.0419	0.1457	-0.8154	-0.4412	-0.1988	0.6308	0.2164	-0.0124	0.4166	-0.046	0.3823	34.8637	30.6238	-31.5917
16	4.0729	-1.273	-1.0455	2.8827	-0.4307	3.6608	-0.211	-0.7926	0.3932	0.4872	0.3433	-0.0408	-0.6848	-0.3707	-0.1312	0.5328	0.1454	-0.0404	0.5434	-0.0783	0.3358	36.5345	22.7982	-21.0567
17	4.8787	0.3741	-1.3964	3.4137	-1.2027	5.8306	0.1466	-0.3865	-0.0769	0.0753	-0.0816	-0.2367	-0.2754	0.1251	-0.0842	0.3273	0.0141	-0.0582	0.2742	0.0112	0.2951	50.0185	6.27	-25.4621
18	3.513	-0.2671	1.634	0.9908	-0.9935	5.626	-0.0901	0.4315	0.4919	-0.2941	-0.151	-0.1567	-0.252	-0.02	0.1283	0.3569	0.0194	0.0313	0.2743	0.0099	0.3399	45.5238	22.8619	-46.4698
19	2.5431	0.3007	-0.9158	7.0759	-1.7463	3.0376	0.4361	-0.3481	0.1564	1.5876	0.0357	0.963	-0.4917	-0.3285	-0.0649	0.6963	-0.0711	0.2903	0.4217	-0.0097	0.4406	82.3579	38.4922	-1.7772
20	1.5818	1.4816	-1.3992	0.9535	-0.8345	0.9597	0.3973	-0.1263	1.4642	1.3657	0.165	1.3561	-0.4167	-0.4039	-0.5789	0.8595	0.0681	0.5418	0.6148	0.0128	1.1757	75.6952	55.7025	-4.6874
21	2.0089	-0.0396	0.3	7.7105	1.5405	4.7753	0.0077	0.212	0.0272	-0.1055	-0.0722	1.0096	0.1374	-0.6013	0.004	0.2576	-0.0251	-0.0151	0.4748	0.1343	0.4659	83.8923	49.5086	-21.2779
22	3.9488	-0.417	0.8555	6.5205	-3.0882	4.6071	0.1064	-0.4773	-0.3097	0.9787	-0.2052	-0.4299	0.0843	0.1764	0.1218	0.5721	-0.054	-0.0887	0.2965	0.0031	0.3486	94.0012	30.441	-3.976

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 144 through 208 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 209 through 279 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 280 through 378 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 379 through 448 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 449 through 486 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 144 through 178 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 179 through 208 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 209 through 268 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 269 through 378 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 379 through 448 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 449 through 486 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 143 through 178 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 179 through 208 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 209 through 238 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 239 through 260 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 261 through 378 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 379 through 448 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 449 through 486 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 143 through 348 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 349 through 387 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 388 through 448 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 449 through 486 )

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