PDB-5klq: Crystal structure of HopZ1a in complex with IP6 and CoA

ID or keywords:

Entry

Database: PDB / ID: 5klq

Title

Crystal structure of HopZ1a in complex with IP6 and CoA

Components

Orf34

Keywords

TRANSFERASE / Ser/Thr acetyltransferase

Function / homology

Function and homology information

O-acetyltransferase activity / host cytoskeleton / inositol hexakisphosphate binding / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / toxin activity / host cell cytoplasm / host cell nucleus / host cell plasma membrane / extracellular region / membrane
Similarity search - Function

Biological species

Pseudomonas syringae pv. syringae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.4 Å

Authors

Zhang, Z.-M. / Song, J.

Citation

Journal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Structure of a pathogen effector reveals the enzymatic mechanism of a novel acetyltransferase family.
Authors: Zhang, Z.M. / Ma, K.W. / Yuan, S. / Luo, Y. / Jiang, S. / Hawara, E. / Pan, S. / Ma, W. / Song, J.

History

Deposition	Jun 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 17, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 31, 2016	Group: Database references
Revision 1.2	Sep 21, 2016	Group: Database references
Revision 1.3	Oct 14, 2020	Group: Derived calculations / Structure summary / Category: chem_comp / pdbx_struct_oper_list Item: _chem_comp.pdbx_synonyms / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4	Mar 6, 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
Revision 1.5	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5klq.cif.gz	376.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5klq.ent.gz	309.8 KB	Display	PDB format
PDBx/mmJSON format	5klq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5klq_validation.pdf.gz	2.6 MB	Display	wwPDB validaton report
Full document	5klq_full_validation.pdf.gz	2.6 MB	Display
Data in XML	5klq_validation.xml.gz	39.2 KB	Display
Data in CIF	5klq_validation.cif.gz	50.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kl/5klq ftp://data.pdbj.org/pub/pdb/validation_reports/kl/5klq	HTTPS FTP

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Related structure data

Related structure data	5klpC C: citing same article (ref.)
Similar structure data	4kav-d 5klp-1 6kze-1 1lqa-2 6tn8-d 4dym-d 7a21-1 5wxl-2 6b97-2 3my0-4 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

5klpC

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) #146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

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)
#146 - Feb 2012
Aminoglycoside Antibiotics
similarity (1)
#93 - Sep 2007
Citrate Synthase
similarity (1)
#154 - Oct 2012
Citric Acid Cycle
similarity (1)
#216 - Dec 2017
Biodegradable Plastic
similarity (1)
#39 - Mar 2003
lac Repressor
similarity (1)

Deposited unit

C: Orf34

A: Orf34

B: Orf34

hetero molecules

118 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: Orf34

hetero molecules

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

2

A: Orf34

hetero molecules

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

3

B: Orf34

hetero molecules

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

Unit cell

Length a, b, c (Å)	49.131, 82.295, 86.268
Angle α, β, γ (deg.)	64.20, 76.69, 89.35
Int Tables number	1
Space group name H-M	P1

#1: Protein	Orf34 Mass: 37983.453 Da / Num. of mol.: 3 / Fragment: residues 29-369 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. syringae (bacteria) Production host: Enterobacteria phage L1 (virus) / References: UniProt: Q6VE93
#2: Chemical	ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE Mass: 660.035 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₈O₂₄P₆
#3: Chemical	ChemComp-COA / COENZYME A Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₃₆N₇O₁₆P₃S
#4: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈O₇

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.9 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG10000. 100mM HEPES, pH 7.0, 200 mM ammonium acetate

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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: Jan 24, 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: 3.4→47.57 Å / Num. obs: 15997 / % possible obs: 97.3 % / Redundancy: 2.5 % / Net I/σ(I): 4.8

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data scaling
PHENIX		phasing
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: HopZ1a

Resolution: 3.4→47.566 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 29.49

	R_factor	Num. reflection	% reflection
R_free	0.2815	1599	10.02 %
R_work	0.2344	-	-
obs	0.2392	15953	98.44 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 3.4→47.566 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7304	0	248	0	7552

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7732
X-RAY DIFFRACTION	f_angle_d	0.9	10552
X-RAY DIFFRACTION	f_dihedral_angle_d	14.935	2727
X-RAY DIFFRACTION	f_chiral_restr	0.043	1173
X-RAY DIFFRACTION	f_plane_restr	0.005	1358

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 (%)
3.4002-3.5099	0.3446	138	0.3103	1289	X-RAY DIFFRACTION	95
3.5099-3.6353	0.2954	139	0.2698	1258	X-RAY DIFFRACTION	98
3.6353-3.7808	0.3303	154	0.2635	1315	X-RAY DIFFRACTION	98
3.7808-3.9528	0.3332	139	0.2605	1291	X-RAY DIFFRACTION	99
3.9528-4.1611	0.2743	154	0.2523	1312	X-RAY DIFFRACTION	98
4.1611-4.4216	0.2814	148	0.2288	1316	X-RAY DIFFRACTION	99
4.4216-4.7627	0.2639	155	0.2188	1290	X-RAY DIFFRACTION	99
4.7627-5.2414	0.2953	144	0.2171	1321	X-RAY DIFFRACTION	99
5.2414-5.9986	0.2947	136	0.2378	1326	X-RAY DIFFRACTION	99
5.9986-7.5527	0.2924	142	0.2394	1317	X-RAY DIFFRACTION	100
7.5527-47.5705	0.2049	150	0.1751	1319	X-RAY DIFFRACTION	99

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	1.3284	-0.4036	2.0288	1.2307	-0.5546	3.3761	0.1138	0.1744	-0.1632	0.1345	-0.3238	-0.4515	0.508	0.7821	0.1007	0.5407	0.1362	0.0871	0.5194	0.513	0.4665	16.6203	-54.5404	-36.5913
2	0.5658	0.4575	-0.4191	2.1283	-0.4076	3.5141	0.2147	-0.1856	-0.3664	-0.0677	-0.2234	0.2279	-0.2409	-0.0277	-0.2978	0.2718	0.0611	0.1453	0.2237	0.1355	0.392	-0.618	-42.4254	-48.2741
3	1.3512	0.4427	0.963	2.0245	-0.4548	2.8831	-0.1373	0.3323	-0.4154	-0.212	0.2915	-0.1861	0.1686	0.3114	0.9387	0.2183	0.1124	0.2477	0.4714	0.1287	0.3556	6.9584	-36.5906	-53.8966
4	1.8261	-0.0378	0.3759	0.9162	-0.2982	1.8553	-0.0737	0.2619	-0.6244	-0.0159	-0.1825	-0.1802	0.1444	0.1798	0.0313	0.2784	-0.0001	0.0775	0.2756	0.117	0.4658	12.9777	-32.378	-54.5904
5	0.9586	0.3184	0.2432	1.0432	0.4758	1.8806	-0.15	-0.1047	-0.0792	-0.0673	-0.1081	0.265	-0.1861	0.0753	-0.4241	0.2503	0.1401	0.23	0.3065	0.0685	0.2896	8.6298	-26.9223	-45.4935
6	2.0382	-0.142	0.3948	1.2729	0.0398	1.1541	0.1453	-0.4252	0.2135	0.1095	0.0987	-0.0275	-0.514	-0.0611	-0.229	0.3712	-0.0327	0.0743	0.28	-0.0198	0.2144	15.8269	-26.2281	-40.3963
7	2.1263	-0.9756	1.6033	3.2226	-0.4389	1.8148	0.0802	-0.7954	-0.2985	0.1191	0.241	0.2309	0.2099	-0.0922	0.1033	0.4958	0.0787	0.0883	0.4404	0.1869	0.4662	17.2433	-36.5363	-25.5962
8	2.105	0.5555	-1.9901	1.8681	-1.0708	3.9372	0.0569	-0.5695	0.2151	-0.7622	0.0779	-0.7551	0.1388	0.7025	0.3114	0.3822	0.0057	0.1842	0.4258	0.2419	0.72	33.452	-41.5731	-39.6033
9	0.9351	-0.4858	0.2297	0.7604	0.0847	0.5238	-0.0066	-0.0817	-0.2746	0.0882	0.201	-0.0347	0.0688	-0.0404	-0.0132	0.0378	0.0572	0.013	0.5749	0.1648	0.4673	9.7416	-50.7357	-34.8305
10	2.7063	0.2574	-0.5116	2.5615	0.116	1.5668	0.2988	0.3187	0.1554	0.1199	-0.1638	-0.3133	0.1384	0.0138	-0.1188	0.3863	-0.0367	-0.1127	0.1648	0.0551	0.3113	20.9865	-24.361	-98.6733
11	2.2007	-1.1167	0.0663	0.9204	0.6711	2.3288	-0.067	-0.103	-0.0612	0.0956	0.0366	-0.1533	0.0048	0.1519	0.039	0.2398	-0.0694	0.0593	0.17	0.0561	0.2365	24.91	-26.4561	-82.4946
12	2.0105	-0.8938	-0.7432	2.7558	0.9306	1.383	-0.3502	-0.2761	0.5808	-0.3812	0.0692	-0.1533	-0.3871	-0.2704	0.2056	0.3995	0.111	-0.2153	0.3354	-0.0562	0.6988	36.3149	-53.2628	-58.688
13	0.8311	-0.3348	0.2061	2.877	0.3996	0.2797	-0.0539	-0.2319	0.0208	0.2263	0.0463	0.2717	-0.0867	-0.2991	-0.6343	0.2143	0.1454	-0.2061	0.2802	0.0086	0.2877	21.8225	-71.2425	-53.1359
14	0.0577	0.0881	-0.1697	1.8192	-0.5105	2.3701	-0.0051	-0.2727	0.4184	-0.0041	-0.0122	0.4806	0.0218	0.1338	0.0633	0.1918	0.0137	0.0105	0.4035	-0.1042	0.3824	29.8477	-78.2654	-54.1497
15	1.4676	0.2828	0.2958	1.9508	-0.6096	3.0457	-0.1777	0.0227	-0.0939	0.2597	-0.1864	-0.1183	-0.1797	0.2386	-1.1268	0.2476	0.1167	0.1487	0.2546	0.0176	0.1168	34.1282	-78.1229	-60.8241
16	2.0785	1.6261	-0.3448	2.4314	-0.0784	1.5151	-0.3293	0.044	-0.2597	-0.387	0.1383	-0.2418	-0.1218	-0.0808	-0.042	0.4093	0.0229	-0.1523	0.3479	-0.0875	0.1635	30.536	-79.7972	-66.9604
17	2.3444	0.7841	0.0912	2.8742	0.1815	2.3154	-0.1341	0.1209	-0.0019	0.1618	0.2457	-0.3467	0.3298	0.2916	0.1195	0.3837	0.0786	-0.0773	0.3333	-0.0422	0.093	35.2928	-80.8649	-65.9935
18	2.7727	-0.067	0.3767	1.1639	-0.3197	1.2242	-0.0494	0.9146	-0.1107	-0.7263	-0.0812	0.0733	0.3677	-0.2126	0.2027	0.644	-0.0372	0.0219	0.567	-0.0321	0.1988	40.0812	-66.8602	-78.3681
19	2.9527	-0.4064	2.018	0.3875	-0.0817	2.9058	0.031	0.2602	0.3424	-0.098	0.1478	-0.3217	0.6163	0.8989	0.3866	0.6194	-0.0443	-0.1191	0.5777	0.0652	0.3796	55.5961	-64.5323	-63.2781
20	2.5687	0.1292	0.6179	0.4904	-0.466	0.6614	-0.1528	-0.4122	0.6801	0.019	-0.0358	0.3533	-0.2121	-0.5455	0.5649	0.2456	-0.0171	-0.1402	0.718	-0.1723	0.4948	32.536	-54.2503	-61.9863

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 46 through 96 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 97 through 137 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 138 through 170 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 171 through 215 )
5	X-RAY DIFFRACTION	5	chain 'C' and (resid 216 through 265 )
6	X-RAY DIFFRACTION	6	chain 'C' and (resid 266 through 311 )
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 312 through 333 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 334 through 350 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 351 through 368 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 43 through 137 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 138 through 368 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 46 through 106 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 107 through 125 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 126 through 195 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 196 through 215 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 216 through 265 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 266 through 293 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 294 through 333 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 334 through 350 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 351 through 368 )

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