PDB-6vvd: Legionella pneumophila Lpg2603 kinase bound to IP6

ID or keywords:

Entry

Database: PDB / ID: 6vvd

Title

Legionella pneumophila Lpg2603 kinase bound to IP6

Components

Dot/Icm T4SS effector

Keywords

TRANSFERASE / phosphorylation / kinase / IP6

Function / homology

Function and homology information

host cell cytoplasmic vesicle / regulation of GTPase activity / small GTPase binding / nucleotide binding
Similarity search - Function

Biological species

Legionella pneumophila (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.65 Å

Authors

Tomchick, D.R. / Tagliabracci, V.S. / Sreelatha, A.

Funding support

United States, 2items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: ALegionellaeffector kinase is activated by host inositol hexakisphosphate.
Authors: Sreelatha, A. / Nolan, C. / Park, B.C. / Pawlowski, K. / Tomchick, D.R. / Tagliabracci, V.S.

History

Deposition	Feb 17, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2020	Provider: repository / Type: Initial release
Revision 1.1	Apr 15, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	May 13, 2020	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0	Oct 14, 2020	Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / struct_site Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1	Oct 11, 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	6vvd.cif.gz	624.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6vvd.ent.gz	438 KB	Display	PDB format
PDBx/mmJSON format	6vvd.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6vvd_validation.pdf.gz	489.2 KB	Display	wwPDB validaton report
Full document	6vvd_full_validation.pdf.gz	491.3 KB	Display
Data in XML	6vvd_validation.xml.gz	2 KB	Display
Data in CIF	6vvd_validation.cif.gz	9.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vv/6vvd ftp://data.pdbj.org/pub/pdb/validation_reports/vv/6vvd	HTTPS FTP

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Related structure data

Related structure data	6vvcSC 6vveC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6vve-d 6wg9-2 6hyi-d 3pve-d 4ljs-d 1psw-d 1lq8-3 4yhs-d 1vis-d 1qu0-3 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

6vvcSC

6vveC

S: Starting model for refinement

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: Dot/Icm T4SS effector

B: Dot/Icm T4SS effector

C: Dot/Icm T4SS effector

hetero molecules

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

1

A: Dot/Icm T4SS effector

hetero molecules

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

2

B: Dot/Icm T4SS effector

hetero molecules

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

3

C: Dot/Icm T4SS effector

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.928, 73.207, 261.249
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Dot/Icm T4SS effector Mass: 37593.328 Da / Num. of mol.: 3 / Fragment: UNP residues 10-322 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: C3927_13135, DI026_05180 / Plasmid: ppSumo / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta / References: UniProt: A0A2S6F2W2, UniProt: Q5ZSB6*PLUS
#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 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	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: 2.23 Å³/Da / Density % sol: 44.84 % / Mosaicity: 0.625 °
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.75 Details: 0.1 M sodium acetate, 0.03 M sodium chloride, 1 mm IP6, 45% ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97927 Å

Detector

Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 15, 2018 / Details: monochromator

Radiation

Monochromator: sagittally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97927 Å / Relative weight: 1

Reflection

Resolution: 2.65→50 Å / Num. obs: 30198 / % possible obs: 99.2 % / Redundancy: 19.1 % / R_merge(I) obs: 0.073 / R_pim(I) all: 0.017 / R_rim(I) all: 0.075 / Χ²: 0.973 / Net I/σ(I): 9.4 / Num. measured all: 575456

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.65-2.7	15.3	1.988	1415	0.541	0.49	2.052	0.922	96.3
2.7-2.74	16.4	1.807	1465	0.645	0.432	1.862	0.891	97.8
2.74-2.8	17	1.531	1491	0.733	0.363	1.576	0.913	98.2
2.8-2.85	17.1	1.255	1430	0.824	0.299	1.292	0.926	98.3
2.85-2.92	16.2	1.024	1510	0.855	0.254	1.057	0.917	98.6
2.92-2.98	19.4	0.916	1455	0.905	0.207	0.94	0.903	99.4
2.98-3.06	19.7	0.733	1494	0.919	0.165	0.752	0.916	99.3
3.06-3.14	19.8	0.52	1493	0.965	0.118	0.534	0.928	99.9
3.14-3.23	19.5	0.373	1492	0.981	0.085	0.383	0.964	99.5
3.23-3.34	19.1	0.257	1511	0.988	0.059	0.265	0.987	99.7
3.34-3.46	19	0.213	1493	0.992	0.049	0.219	1.029	99.7
3.46-3.6	17.6	0.147	1496	0.995	0.035	0.151	1.041	99.2
3.6-3.76	20.4	0.12	1519	0.997	0.027	0.123	1.067	100
3.76-3.96	20.7	0.09	1496	0.998	0.02	0.092	1.119	100
3.96-4.21	21.1	0.069	1525	0.999	0.015	0.071	1.098	100
4.21-4.53	20.6	0.055	1553	0.999	0.012	0.057	1.077	99.8
4.53-4.99	20.3	0.048	1524	0.999	0.011	0.049	1.105	99.5
4.99-5.71	21.9	0.045	1559	0.999	0.01	0.046	0.98	99.9
5.71-7.19	19.7	0.039	1578	0.999	0.009	0.04	0.869	99.7
7.19-50	19.5	0.029	1699	0.999	0.007	0.03	0.755	99.5

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1	refinement
HKL-3000		data scaling
PDB_EXTRACT	3.25	data extraction
HKL-3000		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 6VVC

6vvc

Resolution: 2.65→43.54 Å / SU ML: 0.3097 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.5624
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2805	2056	7.79 %	random
R_work	0.256	24345	-	-
obs	0.2579	26401	87 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 59.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→43.54 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7107	0	108	0	7215

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0031	7418
X-RAY DIFFRACTION	f_angle_d	0.5861	10074
X-RAY DIFFRACTION	f_chiral_restr	0.0409	1023
X-RAY DIFFRACTION	f_plane_restr	0.0035	1280
X-RAY DIFFRACTION	f_dihedral_angle_d	13.6828	2776

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 (%)
2.65-2.72	0.3316	64	0.3181	757	X-RAY DIFFRACTION	41.61
2.72-2.78	0.4165	85	0.3058	1011	X-RAY DIFFRACTION	54.91
2.78-2.86	0.2858	99	0.2985	1169	X-RAY DIFFRACTION	64.63
2.86-2.94	0.3419	114	0.3065	1364	X-RAY DIFFRACTION	73.1
2.94-3.04	0.3325	130	0.3091	1521	X-RAY DIFFRACTION	84.71
3.04-3.15	0.3625	143	0.2958	1700	X-RAY DIFFRACTION	91.78
3.15-3.27	0.3164	150	0.28	1766	X-RAY DIFFRACTION	95.94
3.27-3.42	0.2975	150	0.2711	1785	X-RAY DIFFRACTION	97.63
3.42-3.6	0.2821	156	0.2799	1841	X-RAY DIFFRACTION	98.42
3.6-3.83	0.3346	157	0.2611	1856	X-RAY DIFFRACTION	99.9
3.83-4.12	0.2444	158	0.241	1875	X-RAY DIFFRACTION	100
4.12-4.54	0.2251	159	0.221	1874	X-RAY DIFFRACTION	99.85
4.54-5.19	0.2426	158	0.2124	1880	X-RAY DIFFRACTION	99.61
5.19-6.54	0.2787	163	0.2547	1924	X-RAY DIFFRACTION	99.95
6.54-43.54	0.2515	170	0.2364	2022	X-RAY DIFFRACTION	99.41

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	0.732550803363	-0.100115498948	0.590669025158	0.399060730441	-0.164741253292	0.991658597868	-0.0389245211939	-0.142421384613	-0.0176200867259	0.0729447961018	0.0453251804362	-0.0668891235229	0.0159150324297	0.180736795245	-0.0878452538252	0.359787744688	0.154437112899	-0.19446931098	0.80834353094	0.0154929596447	0.263845278397	28.9605809526	-19.3297840943	-17.7403636401
2	2.76392636459	-0.0784755117051	0.854280955321	1.62106985358	-0.0746783675175	1.07975245586	0.0313047141821	-0.788270199117	-0.335494369643	0.269072550433	0.172935535842	0.205616010371	0.427949641153	-0.179005956636	-0.236292701681	0.279813364683	0.0471317770628	-0.0847174030592	0.418941751096	0.105882007136	0.237854286124	13.6311352468	-17.1338413295	-22.8041027405
3	2.58712325909	-0.505576639152	-0.325484292175	2.2655781374	-0.950938021056	4.3802356815	-0.0102215707723	-0.535485234834	0.158799470797	0.156514455344	0.0948156879831	-0.0336754136185	-0.164307143132	-0.0196839095542	-0.106319276418	0.143976583511	-0.00082282608916	-0.0249756118099	0.255965412024	-0.059853137528	0.113244827745	12.8843696937	-8.06395965199	-28.6718039217
4	2.99955852576	-1.15870409509	0.290381412612	1.25007743337	-1.2011559487	1.79913306371	0.29055640521	0.201749729703	-0.185271546825	-0.486138021082	-0.126548768144	0.300517400969	0.352323758557	0.0927134097901	0.0384056375313	0.200190652921	0.0993525489944	-0.0829936434286	0.126089092457	-0.0509243875413	0.159917833767	11.437392532	-11.0669523972	-40.732570883
5	3.25622571757	0.620186775671	-0.259516585323	1.72593824078	0.274098253	1.28681620536	0.281926114752	0.640218806852	-0.0670424961775	-0.961412742418	-0.433061382889	0.308065916473	0.316444594536	-0.0511751979242	0.0975160410003	0.736144869866	0.257852039239	-0.0283322666098	0.322959931625	0.0272285617036	0.282543801045	8.38169992937	-2.69835206082	-54.7046446015
6	1.28199372699	-1.7426140421	1.11217935822	2.38901711212	-1.9101260558	9.0073504963	-0.020906343313	0.248325432291	0.190765185227	-0.184186299843	-0.507661902092	-0.92257708911	-0.535368793507	1.05106420955	0.724418648867	0.651144418581	0.159302553121	0.279700018231	0.500071566887	0.334775963794	0.680294412556	18.451568633	4.56972888155	-51.958863458
7	0.605117784038	0.105168805917	-0.887410916165	1.89594426655	-0.29217513191	1.91758570368	0.136624622137	0.775540247596	0.363437029591	-0.697100320798	-0.210589711539	-0.395843129669	-0.192566747569	-0.537848538479	0.00958940692285	0.453995585552	0.232295018863	0.19151765969	0.544302828896	0.212825713192	0.478157411378	42.6415874672	-8.26540907881	-72.2716600771
8	1.48832900097	0.583963582995	-0.0158593613349	0.93110074702	-0.667250904612	1.82385263318	-0.104329890544	0.214318355647	-0.31100495351	-0.308247586809	0.064788242015	0.0192055298376	0.676505456276	-0.676543318053	0.0215163467164	0.292000077486	-0.170567746307	0.00768279669315	0.296958096072	-0.0266634944805	0.384602034841	37.4397436157	-24.1844863698	-55.8531051156
9	1.55825233267	-0.0952905641653	0.494727455518	1.02073742923	0.342449661678	2.88945335235	0.0204276344087	-0.0310491240018	0.0381047283689	0.174205527688	-0.159269253323	-0.302212292933	0.0623786923793	-0.470296545961	0.0237940972886	0.0923936795808	0.0284727745705	-0.0587225566967	0.132620343753	-0.0467114286225	0.294398730541	39.1900970588	-16.9925314136	-43.5412073053
10	1.79668584235	0.342131279068	0.409416527408	5.87159918718	0.608161772233	0.515170493997	0.0710662635323	0.121774363632	0.0972027127426	0.156385300745	-0.037432533198	0.658472806456	-0.459075095312	-0.633839830342	0.0348077362334	0.942211989469	0.384009043076	-0.103202945489	0.777270852449	-0.17582480346	0.436285165014	28.7438889	23.2302053727	-33.0542056988
11	2.56814610902	-1.37150839726	-2.8877268234	1.02095280976	1.8593905664	4.04137684583	0.0758218094369	0.350954774685	-0.0133244107653	-0.794516818095	-0.31919082525	-0.0400758963379	-0.0294559886917	-0.245644135735	0.252980007051	1.01815629866	0.508714789722	-0.138570201317	0.807818969768	-0.2163202063	0.729186780929	31.5618929994	18.7192710586	-30.0904301374
12	2.29412945215	0.192355227886	0.00354073478286	1.96357692338	0.0843359572607	1.80411586503	-0.0619932192592	0.0531193834178	0.267402223479	-0.352146717713	-0.0628680933121	0.340429100715	-0.397645959849	-0.132217992412	0.1003942817	0.91830391023	0.337087008869	0.139628070008	0.626633845118	-0.102437356667	0.759206959482	34.8035584616	24.6884341832	-27.0325008869
13	1.80656851297	-0.887789452216	-0.592009127875	2.5002165391	1.60935645641	1.49233697677	0.34965728899	0.104710414529	0.300019657474	-0.47972067559	-0.0146636371897	-0.356290578848	-0.395086434045	0.182696947199	-0.271004152467	0.735876104148	0.135619428303	0.0324812900087	0.309207917619	-0.188864719024	0.538450860963	42.7185945113	20.1759251904	-21.517366245
14	0.686321370946	-0.401639937796	-1.46562720664	0.289260057552	0.51119419958	5.29328647873	0.136044319869	-0.480257647183	0.630976439767	-0.25632481	0.609307583493	-1.09782087795	-1.04105070337	1.23930223399	-0.735188675033	1.01787767798	0.0731969196678	0.197277512152	0.811464106869	-0.432995533538	1.07493461654	48.6291538836	27.4008565084	-21.3268022892
15	0.547377648204	0.0515617241242	-0.463704532617	0.475058486733	0.355384605495	2.21636883994	0.154296355923	-0.178976105297	0.395365809571	-0.221608819358	0.117676021369	-0.310030436418	-0.778592945247	0.0663838148909	-0.18090290507	0.519731644408	0.056085545429	0.0620152323229	0.773731911778	-0.51168575295	0.797522767924	45.1796254441	27.1083490315	-7.19481277115
16	4.46955925869	0.707840689675	3.63779360196	1.47851922182	1.00508869597	3.23544902328	0.319468054278	-0.785656071038	-0.472908771717	0.48116636862	0.255122643074	-0.41764379051	0.415537815945	-0.348608307791	-0.393498190926	0.488633985286	0.168569539752	-0.124788616549	1.37408521449	-0.437115761884	0.696849457522	46.0313870717	19.4629676306	2.69178733622
17	0.895523189852	0.331193734024	0.388258203196	1.15521395673	-0.826959075872	1.08400912719	-0.0457425887693	-0.597269906177	0.202447787492	0.844896046975	0.0909032825178	0.191362665615	-0.164853308373	-0.429464977209	-0.0296167883999	0.869541984603	0.104609842099	0.0278202930098	1.56741159136	-0.305165330637	0.692066335022	40.7351275832	24.4484472885	11.505440383
18	0.578545540344	-0.200175203488	-0.404642630809	0.0692248959399	0.140040560995	0.282928694759	0.22751048719	0.0123605936005	0.103773453606	-0.218961088614	-0.0628838894626	-0.0561180576018	-0.322580410119	-0.108843873759	-0.0816451028171	0.669205738871	0.15840428654	-0.0610456876327	1.31730455607	-0.655395236822	0.969873205005	29.5244669968	31.2492446957	12.4671887313

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 24 through 66 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 67 through 142 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 143 through 194 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 195 through 259 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 260 through 291 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 292 through 317 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 24 through 165 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 166 through 195 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 196 through 322 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 24 through 37 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 38 through 53 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 54 through 97 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 98 through 154 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 155 through 178 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 179 through 228 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 229 through 280 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 281 through 309 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 310 through 322 )

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