PDB-5klp: Crystal structure of HopZ1a in complex with IP6

ID or keywords:

Entry

Database: PDB / ID: 5klp

Title

Crystal structure of HopZ1a in complex with IP6

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 /

SAD / Resolution: 2.002 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 10, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 17, 2016	Group: Database references
Revision 1.2	Aug 31, 2016	Group: Database references
Revision 1.3	Sep 21, 2016	Group: Database references
Revision 1.4	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Oct 14, 2020	Group: Structure summary / Category: chem_comp / Item: _chem_comp.pdbx_synonyms
Revision 1.6	Oct 23, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5klp.cif.gz	384.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5klp.ent.gz	313.9 KB	Display	PDB format
PDBx/mmJSON format	5klp.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5klp_validation.pdf.gz	2.1 MB	Display	wwPDB validaton report
Full document	5klp_full_validation.pdf.gz	2.1 MB	Display
Data in XML	5klp_validation.xml.gz	43.1 KB	Display
Data in CIF	5klp_validation.cif.gz	60.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/kl/5klp ftp://data.pdbj.org/pub/pdb/validation_reports/kl/5klp	HTTPS FTP

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Related structure data

Related structure data	5klqC C: citing same article (ref.)
Similar structure data	4u0i-d 5klq-1 3ws4-3 5y61-1 7a21-1 1rr6-d 4fcm-d 5wad-1 5caj-1 2xnj-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

5klqC

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: Orf34

B: Orf34

C: Orf34

hetero molecules

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

1

A: Orf34

hetero molecules

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

2

B: Orf34

hetero molecules

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

3

C: Orf34

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.153, 99.777, 71.915
Angle α, β, γ (deg.)	90.00, 103.44, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Orf34 Mass: 38196.559 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-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 535 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.23 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 18-26% PEG 550 MME, 0.1 M sodium citrate, pH 5.2, 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: Jul 11, 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→50 Å / Num. obs: 119760 / % possible obs: 98.5 % / Redundancy: 3.6 % / Net I/σ(I): 17.3

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Processing

Software

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

Refinement

Method to determine structure:

SAD / Resolution: 2.002→49.889 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2136	3648	3.05 %
R_work	0.1683	-	-
obs	0.1697	119723	92.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.002→49.889 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7159	0	186	535	7880

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7476
X-RAY DIFFRACTION	f_angle_d	1.207	10157
X-RAY DIFFRACTION	f_dihedral_angle_d	17.37	2685
X-RAY DIFFRACTION	f_chiral_restr	0.095	1115
X-RAY DIFFRACTION	f_plane_restr	0.005	1327

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 (%)
2.002-2.0284	0.2937	116	0.2674	3937	X-RAY DIFFRACTION	82
2.0284-2.0562	0.3207	135	0.2413	4261	X-RAY DIFFRACTION	88
2.0562-2.0856	0.2764	136	0.224	4399	X-RAY DIFFRACTION	90
2.0856-2.1167	0.2458	144	0.2227	4410	X-RAY DIFFRACTION	91
2.1167-2.1498	0.224	142	0.2124	4330	X-RAY DIFFRACTION	91
2.1498-2.185	0.271	127	0.2056	4417	X-RAY DIFFRACTION	91
2.185-2.2227	0.2507	139	0.2005	4362	X-RAY DIFFRACTION	91
2.2227-2.2631	0.2614	143	0.2001	4420	X-RAY DIFFRACTION	91
2.2631-2.3066	0.26	137	0.1949	4435	X-RAY DIFFRACTION	91
2.3066-2.3537	0.2414	143	0.1815	4387	X-RAY DIFFRACTION	92
2.3537-2.4049	0.2493	139	0.1866	4499	X-RAY DIFFRACTION	92
2.4049-2.4608	0.226	138	0.1751	4457	X-RAY DIFFRACTION	92
2.4608-2.5224	0.2628	138	0.1725	4399	X-RAY DIFFRACTION	93
2.5224-2.5906	0.2403	147	0.1778	4456	X-RAY DIFFRACTION	92
2.5906-2.6668	0.2068	140	0.1728	4560	X-RAY DIFFRACTION	93
2.6668-2.7529	0.2822	142	0.1688	4455	X-RAY DIFFRACTION	93
2.7529-2.8512	0.2184	138	0.1712	4537	X-RAY DIFFRACTION	93
2.8512-2.9654	0.1789	140	0.1707	4522	X-RAY DIFFRACTION	94
2.9654-3.1003	0.2074	143	0.1594	4488	X-RAY DIFFRACTION	94
3.1003-3.2637	0.2061	146	0.1641	4588	X-RAY DIFFRACTION	94
3.2637-3.4682	0.2175	139	0.1566	4531	X-RAY DIFFRACTION	95
3.4682-3.7359	0.188	147	0.145	4639	X-RAY DIFFRACTION	95
3.7359-4.1117	0.168	143	0.1446	4557	X-RAY DIFFRACTION	95
4.1117-4.7063	0.1662	149	0.136	4657	X-RAY DIFFRACTION	96
4.7063-5.9279	0.1945	143	0.1527	4651	X-RAY DIFFRACTION	96
5.9279-49.904	0.2034	154	0.1648	4721	X-RAY DIFFRACTION	98

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	2.662	-0.2178	0.3708	2.2782	-0.6965	2.2095	0.0592	0.4998	-0.1401	-0.4621	0.084	-0.1329	0.1901	0.1852	-0.1525	0.2948	-0.0396	0.1054	0.3425	-0.0022	0.2953	19.5766	-1.695	-24.2599
2	1.0455	0.0403	0.131	2.0191	-0.2547	1.0451	-0.0465	-0.145	0.1219	0.1468	0.0676	-0.0961	-0.0945	0.1035	-0.0221	0.1613	0.0298	-0.0175	0.239	-0.0691	0.1742	12.3269	-8.2241	-0.5461
3	1.8582	-0.3485	-0.2536	1.326	-0.2477	1.1753	-0.1432	-0.1283	0.0239	0.0639	0.2149	0.1398	0.06	-0.0426	-0.063	0.1302	0.0235	-0.0009	0.1365	-0.0168	0.1518	-2.2088	-10.1899	-3.7287
4	3.9794	0.3857	0.6731	0.6818	0.0491	1.3269	-0.22	0.3524	0.6654	-0.2209	0.1979	0.1533	-0.1325	0.0364	-0.0137	0.2277	-0.0532	-0.0152	0.2084	0.0456	0.3351	2.7933	1.8003	-20.1565
5	2.9479	0.6698	-0.5079	1.989	-0.9993	2.1683	-0.0071	0.2613	0.1091	-0.155	0.0844	0.2038	-0.324	-0.0594	-0.0285	0.2931	0.0346	-0.0722	0.2488	0.0115	0.2184	-43.3935	25.5144	-9.6737
6	1.3303	-0.5028	0.1891	0.8366	0.1173	2.4764	-0.0071	-0.0733	-0.1443	-0.0016	0.0972	0.152	0.1239	-0.242	-0.1055	0.1857	-0.0117	0.003	0.1753	0.0036	0.2573	-37.5261	9.852	7.7982
7	1.9149	-0.1847	0.2999	0.9538	-0.1055	1.9631	-0.105	-0.0552	-0.1482	0.0024	0.0449	0.0623	0.0323	0.1338	0.0458	0.1408	0.0184	0.0118	0.1289	0.008	0.1502	-22.8976	10.453	8.9977
8	1.93	0.1108	0.3982	0.8845	0.0265	0.8922	-0.1013	0.2947	0.0221	-0.1337	0.0545	0.0014	-0.0798	0.1893	0.0588	0.1891	-0.0239	-0.0019	0.2058	-0.0138	0.1876	-23.7719	18.8506	-5.1732
9	3.0909	-0.2873	0.0839	2.104	-0.1476	1.5902	-0.177	0.1342	-0.3917	-0.3764	0.0803	0.1124	0.386	-0.2426	0.0803	0.3147	-0.0702	0.0485	0.2536	-0.0191	0.2196	-50.2477	10.4556	-43.9937
10	1.2031	0.413	-0.445	2.2677	-0.6407	2.1138	-0.1667	-0.2736	0.0889	0.3249	0.1097	0.2113	-0.0329	-0.1932	-0.0336	0.2532	0.0478	0.0265	0.2882	-0.0513	0.1307	-46.7573	26.1282	-31.7762
11	1.4137	0.1244	0.098	1.0677	-0.8148	1.557	-0.1141	-0.1688	0.3548	0.2965	0.0474	-0.1645	-0.2178	-0.1536	-0.0151	0.2834	0.0461	-0.0471	0.1933	-0.1001	0.2006	-38.98	35.8328	-37.8301
12	1.5629	-0.2925	-0.5715	1.8618	0.1658	1.6921	-0.1266	-0.2519	0.1681	0.0777	0.0928	-0.4397	0.0499	0.3031	0.0454	0.17	0.0201	-0.0323	0.2425	-0.0367	0.2384	-27.6158	25.1977	-39.7638
13	0.5828	-0.1293	-0.0792	1.0831	0.4188	1.6821	-0.3222	0.5121	-0.2595	-0.3474	0.1061	0.1584	0.5225	-0.3548	0.1005	0.3408	-0.0391	0.0627	0.2324	-0.0018	0.1169	-43.1833	10.6383	-43.1347

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 45 through 87 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 88 through 164 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 165 through 293 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 294 through 369 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 46 through 87 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 88 through 151 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 152 through 265 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 266 through 369 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 43 through 95 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 96 through 117 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 118 through 170 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 171 through 329 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 330 through 368 )

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