PDB-5w3y: Crystal structure of PopP2 C321A in complex with IP6 and AcCoA

ID or keywords:

Entry

Database: PDB / ID: 5w3y

Title

Crystal structure of PopP2 C321A in complex with IP6 and AcCoA

Components

PopP2 protein

Keywords

TRANSFERASE / PopP2 / ip6 / AcCoA / YopJ / effector

Function / homology

Serine/Threonine acetyltransferase, YopJ / YopJ Serine/Threonine acetyltransferase / acyltransferase activity / ACETYL COENZYME *A / INOSITOL HEXAKISPHOSPHATE / PopP2 protein

Function and homology information

Biological species

Ralstonia solanacearum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 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	5w3y.cif.gz	535.1 KB	Display	PDBx/mmCIF format
PDB format	pdb5w3y.ent.gz	441.1 KB	Display	PDB format
PDBx/mmJSON format	5w3y.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5w3y_validation.pdf.gz	4.1 MB	Display	wwPDB validaton report
Full document	5w3y_full_validation.pdf.gz	4.1 MB	Display
Data in XML	5w3y_validation.xml.gz	56.1 KB	Display
Data in CIF	5w3y_validation.cif.gz	76.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/w3/5w3y ftp://data.pdbj.org/pub/pdb/validation_reports/w3/5w3y	HTTPS FTP

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Related structure data

Related structure data	5w3tSC 5w3xC 5w40C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5w40-3 5w3t-3 5w40-1 6c2z-d 3pcs-2 5qjz-1 1m15-d 5qjo-1 6c2h-d 2o1h-d 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

5w3tSC

5w3xC

5w40C

C: citing same article (ref.)

S: Starting model for refinement

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

161 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
40.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: PopP2 protein

hetero molecules

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

3

C: PopP2 protein

hetero molecules

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

4

D: PopP2 protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.385, 79.876, 77.746
Angle α, β, γ (deg.)	112.33, 111.65, 103.39
Int Tables number	1
Space group name H-M	P1

#1: Protein	PopP2 protein Mass: 38666.594 Da / Num. of mol.: 4 / Mutation: C253A 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-ACO / ACETYL COENZYME A Mass: 809.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₃H₃₈N₇O₁₇P₃S / Feature type*: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.44 Å³/Da / Density % sol: 49.59 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop 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: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 23, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9774 Å / Relative weight: 1
Reflection	Resolution: 2.15→50 Å / Num. obs: 77404 / % possible obs: 97.7 % / Redundancy: 1.9 % / R_merge(I) obs: 0.05 / Net I/σ(I): 9.6
Reflection shell	Resolution: 2.15→2.23 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.501 / Mean I/σ(I) obs: 1.1 / % possible all: 96.5

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data scaling
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5w3t

5w3t

Resolution: 2.2→39.085 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 24.76

	R_factor	Num. reflection	% reflection
R_free	0.225	1900	2.62 %
R_work	0.1827	-	-
obs	0.1839	72555	97.75 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.2→39.085 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10011	0	268	460	10739

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	10444
X-RAY DIFFRACTION	f_angle_d	1.157	14217
X-RAY DIFFRACTION	f_dihedral_angle_d	13.436	3810
X-RAY DIFFRACTION	f_chiral_restr	0.053	1620
X-RAY DIFFRACTION	f_plane_restr	0.005	1849

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 (%)
2.2-2.255	0.2794	128	0.2584	5033	X-RAY DIFFRACTION	97
2.255-2.316	0.2971	140	0.2455	4978	X-RAY DIFFRACTION	97
2.316-2.3841	0.2965	140	0.244	5067	X-RAY DIFFRACTION	97
2.3841-2.4611	0.2786	142	0.2359	4980	X-RAY DIFFRACTION	97
2.4611-2.549	0.2959	124	0.2167	5056	X-RAY DIFFRACTION	98
2.549-2.651	0.3072	136	0.2122	5092	X-RAY DIFFRACTION	98
2.651-2.7717	0.2624	137	0.208	5046	X-RAY DIFFRACTION	98
2.7717-2.9177	0.2693	144	0.2062	5063	X-RAY DIFFRACTION	98
2.9177-3.1005	0.2356	125	0.2073	5086	X-RAY DIFFRACTION	98
3.1005-3.3398	0.2523	131	0.1946	5056	X-RAY DIFFRACTION	98
3.3398-3.6756	0.2224	132	0.1805	5116	X-RAY DIFFRACTION	99
3.6756-4.2069	0.1881	142	0.1595	5094	X-RAY DIFFRACTION	99
4.2069-5.2982	0.1809	135	0.1481	5034	X-RAY DIFFRACTION	98
5.2982-39.091	0.1932	144	0.1557	4954	X-RAY DIFFRACTION	96

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	4.0629	-2.2973	2.7373	4.2803	-2.8335	6.293	0.862	0.4283	-0.475	-1.1724	-0.1725	1.2994	0.0971	-0.2392	-0.6648	0.7197	0.0942	-0.2107	0.4824	-0.0713	0.5349	0.5423	-7.7299	39.4724
2	1.3805	-1.9199	1.8553	7.6456	-4.5524	4.7498	0.2655	0.1973	-0.1876	-0.5883	-0.3462	0.0959	0.511	0.371	0.0891	0.3345	0.0027	-0.001	0.3556	-0.0327	0.2681	14.3832	-8.4818	47.6205
3	5.3716	0.3615	-0.5441	6.3548	1.1493	5.3015	0.1023	0.3282	0.0776	-0.9374	0.1079	-0.6935	-0.5338	0.9762	-0.2488	0.4996	-0.0237	0.1055	0.5601	0.0515	0.3736	21.9126	4.0793	40.672
4	2.5219	0.8908	0.6887	4.2207	-0.3351	2.4201	-0.0376	0.1351	0.1464	-0.3603	0.0871	-0.4972	-0.4345	0.5907	-0.0421	0.4033	-0.0851	0.0928	0.457	-0.0307	0.3337	24.6801	11.4774	53.8476
5	2.3314	-0.2736	-0.1767	6.9118	2.2335	4.554	-0.0158	-0.1518	-0.1089	0.0871	0.1048	-0.1642	0.1368	0.3428	-0.1152	0.2382	-0.0017	-0.0345	0.3938	0.0499	0.236	18.3212	-5.3652	66.9204
6	4.497	-1.8139	1.7706	2.5117	-0.8826	5.6778	0.401	0.4743	-0.0553	-0.5709	-0.2478	0.1439	-0.2981	-0.0434	-0.1501	0.4836	0.068	-0.0643	0.2925	-0.0661	0.3218	6.6493	-2.9856	42.8989
7	7.2018	-5.6388	-7.0685	5.1857	6.7606	8.8341	-0.184	0.1083	-0.0939	0.5924	-0.3052	0.2346	-0.0424	-0.6927	0.4184	0.4761	0.0639	-0.0078	0.4288	-0.0568	0.5038	-29.7519	19.208	83.8516
8	5.7942	-2.9662	-3.3749	3.2084	3.9513	5.0449	0.1395	0.4759	-0.0162	-0.1105	-0.3058	-0.023	0.0245	-0.0902	0.1503	0.4575	0.0327	-0.0453	0.3222	0.0305	0.3337	-18.7848	19.4375	72.8323
9	3.9417	0.1116	-0.4788	4.9669	-0.6336	1.872	-0.1595	0.6954	1.9615	-0.2196	-0.2541	-1.2813	-1.1261	0.3815	0.4716	0.8221	0.0222	0.0053	0.4928	0.2163	1.1628	-14.1544	34.7943	74.4248
10	3.4616	0.5275	-0.0474	4.9441	1.461	4.713	0.0161	-0.103	1.8844	0.249	-0.2216	-1.3308	-0.4497	-0.0401	-0.0851	0.6196	-0.0474	-0.1039	0.3117	0.034	1.4049	-4.3868	34.49	77.2694
11	1.0788	1.729	-0.2864	4.4689	0.48	0.5696	-0.2609	0.8569	1.6877	-0.421	-0.4934	-0.5276	-1.0014	0.0543	0.2173	0.8267	-0.0102	-0.0592	0.4736	0.4732	1.4919	-1.0567	31.3311	69.533
12	2.7865	2.4727	-1.5345	3.5168	-0.4832	1.5055	-0.166	-0.259	1.5472	0.2128	-0.1918	-1.3526	-0.6077	0.8838	0.1927	0.6147	-0.1777	-0.1437	0.5973	0.0938	1.4273	4.9571	28.9641	78.682
13	2.254	-1.469	2.0959	4.0779	0.854	4.031	0.3614	0.4576	0.8372	-0.2139	-0.2975	-0.3117	-0.1844	0.3868	-0.1327	0.4268	0.0063	0.0708	0.4134	0.1292	0.4906	3.2519	14.6616	73.2146
14	5.4658	-1.5555	0.532	1.7514	0.7279	1.2352	-0.2078	0.3329	-0.2044	-0.2223	0.016	-0.0347	-0.0998	0.1821	0.1934	0.366	-0.0056	0.0264	0.2653	0.0734	0.2971	-7.1786	10.7163	74.7868
15	8.1122	-2.2196	-0.2984	4.1119	-0.6493	9.2507	-0.4509	-0.3601	1.1181	0.3153	0.3393	-0.2612	-0.842	0.0528	0.1361	0.5795	0.1616	-0.1193	0.3376	-0.1135	0.5267	-27.2632	29.8286	82.5515
16	4.5965	-0.8051	2.7663	2.1273	-1.0298	5.1947	0.0253	-0.457	0.0201	0.1674	0.0724	-0.1313	0.3267	-0.5167	-0.0908	0.3796	-0.0111	0.0124	0.2894	-0.0354	0.2795	3.9829	-1.6142	120.3118
17	5.723	0.9453	-1.8395	5.7146	0.7937	6.9511	0.0848	-0.3844	0.4743	0.5983	-0.1572	0.0763	-1.145	0.0848	0.0434	0.6035	0.023	-0.0991	0.3936	-0.0653	0.4132	12.7206	15.5285	121.6276
18	4.0494	2.1234	-0.384	3.5413	0.078	3.2598	0.0875	-0.3459	0.501	0.1877	-0.1403	-0.3609	-0.672	0.2711	0.0729	0.4764	-0.0462	-0.0333	0.3456	-0.0543	0.4851	17.9635	17.7925	110.0673
19	4.6797	2.275	1.6721	7.3998	1.8057	3.4776	0.0716	0.0871	0.6309	-0.0318	-0.201	-0.7864	-0.8148	0.5078	0.1054	0.5619	-0.0989	0.0339	0.3659	0.046	0.5292	18.0409	19.7834	99.0777
20	5.9335	0.8575	-1.0633	3.5317	-0.3468	4.7348	0.0126	0.0772	0.2529	-0.0939	0.035	0.0523	-0.2887	-0.3243	-0.061	0.3258	0.0509	-0.0442	0.2911	-0.0052	0.2207	2.2422	7.5039	95.5923
21	3.2754	-1.6813	1.5134	2.7941	-2.07	5.0247	-0.0603	-0.2542	0.0255	0.2844	0.0892	-0.1835	0.1424	0.3629	-0.0467	0.3096	0.0007	-0.0139	0.2377	-0.0133	0.2726	8.9399	-0.3949	121.1269
22	3.9197	-3.918	-1.199	5.0012	3.3257	4.1449	-0.9947	0.1057	-0.9164	0.3565	0.0554	0.2247	1.3448	0.3732	0.8786	0.4942	-0.004	0.0443	0.2911	-0.0196	0.5289	37.0389	-34.6443	79.698
23	7.0479	-0.9529	-2.4237	2.3967	1.1329	2.1006	-0.293	-0.7259	-0.4789	0.2449	0.193	0.1026	0.5279	0.2061	0.0977	0.4011	0.0103	-0.0282	0.3751	-0.0099	0.3207	34.6846	-23.3874	90.7496
24	2.274	-0.1016	-0.8347	4.1223	0.0188	1.8194	0.121	-0.3644	0.275	0.1919	-0.0058	-0.5184	-0.1733	0.2887	-0.1257	0.3218	-0.03	-0.0292	0.4371	-0.0801	0.385	44.1643	-4.5354	87.2239
25	2.8463	0.2936	-1.3192	6.6252	-0.9254	4.6422	-0.0013	-0.2152	-0.0015	0.3135	0.0122	0.0385	-0.0678	-0.2383	0.016	0.2404	0.0116	0.0239	0.3666	-0.0551	0.3146	21.956	-7.8332	91.3822
26	2.1431	-1.996	-1.84	3.6852	2.0647	4.7118	-0.1844	-0.075	-0.4091	0.1088	0.0056	-0.1024	0.5036	0.4035	0.1146	0.3616	0.0259	0.0063	0.2797	0.0379	0.3626	38.3361	-26.4883	81.6563

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 143 through 178 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 179 through 208 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 209 through 238 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 239 through 378 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 379 through 448 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 449 through 486 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 144 through 178 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 179 through 208 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 209 through 238 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 239 through 288 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 289 through 320 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 321 through 376 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 377 through 397 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 398 through 467 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 468 through 486 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 144 through 208 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 209 through 238 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 239 through 348 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 349 through 387 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 388 through 448 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 449 through 488 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 144 through 178 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 179 through 208 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 209 through 378 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 379 through 448 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 449 through 487 )

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