PDB-6yvc: Crystal structure of the small alarmone hydrolase (SAH) of Pseudo...

ID or keywords:

Entry

Database: PDB / ID: 6yvc

Title

Crystal structure of the small alarmone hydrolase (SAH) of Pseudomonas aeruginosa

Components

Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

Keywords

HYDROLASE / Alarmone / pppGpp / Pseudomonas aeruginosa

Function / homology

: / HD domain / hydrolase activity / : / Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

Function and homology information

Biological species

Pseudomonas aeruginosa (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Altegoer, F. / Bange, G.

Citation

Journal: Mol.Microbiol. / Year: 2021
Title: Dual role of a (p)ppGpp- and (p)ppApp-degrading enzyme in biofilm formation and interbacterial antagonism.
Authors: Steinchen, W. / Ahmad, S. / Valentini, M. / Eilers, K. / Majkini, M. / Altegoer, F. / Lechner, M. / Filloux, A. / Whitney, J.C. / Bange, G.

History

Deposition	Apr 28, 2020	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 12, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 13, 2021	Group: Data collection / Database references Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Jan 24, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yv/6yvc ftp://data.pdbj.org/pub/pdb/validation_reports/yv/6yvc	HTTPS FTP

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Related structure data

Related structure data	5xnxS S: Starting model for refinement
Similar structure data	6yvc-3 6xyk-d 1kuk-d 1u71-d 1pd8-d 1v2o-d 5xw8-d 4ktu-d 3d80-d 4kfj-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

5xnxS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

B: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

C: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

D: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

hetero molecules

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

1

A: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

hetero molecules

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

2

B: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

hetero molecules

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

3

C: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

hetero molecules

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

4

D: Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	85.330, 85.380, 122.170
Angle α, β, γ (deg.)	90.000, 102.059, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

Components on special symmetry positions

ID	Model	Components
1	1	A-423- HOH
2	1	B-510- HOH
3	1	D-488- HOH

#1: Protein	Bifunctional (P)ppGpp synthetase/guanosine-3',5'-bis(Diphosphate) 3'-pyrophosphohydrolase Mass: 21601.330 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: C0044_03060, CGU42_31275, DT376_11420, DY930_06745, DZ962_15010, ECC04_012485, F3H14_24895, IPC116_15200, IPC1481_11715, IPC1509_07345, IPC36_18005, PAMH19_0488 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A071L0I0
#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 854 / Source method: isolated from a natural source / Formula: H₂O
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: 2.63 Å³/Da / Density % sol: 53.16 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 2.0 M sodium formate and 0.1 M sodium acetate pH 4.6

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.072 Å / Relative weight: 1
Reflection	Resolution: 1.85→45.78 Å / Num. obs: 72548 / % possible obs: 99.13 % / Redundancy: 3.7 % / B_iso Wilson estimate: 20.16 Å² / CC_1/2: 0.99 / R_merge(I) obs: 0.147 / Net I/σ(I): 8.09
Reflection shell	Resolution: 1.85→1.92 Å / R_merge(I) obs: 0.622 / Mean I/σ(I) obs: 1.92 / Num. unique obs: 7192 / CC_1/2: 0.69

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
PHENIX	1.17.1_3660	phasing
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5XNX

5xnx

Resolution: 1.85→45.78 Å / SU ML: 0.2414 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.3129
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2219	3627	5 %
R_work	0.1912	68910	-
obs	0.1928	72537	99.14 %

Solvent computation

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

Displacement parameters

B_iso mean: 27.14 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→45.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5553	0	4	854	6411

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0048	5669
X-RAY DIFFRACTION	f_angle_d	0.7374	7692
X-RAY DIFFRACTION	f_chiral_restr	0.0415	844
X-RAY DIFFRACTION	f_plane_restr	0.0051	1015
X-RAY DIFFRACTION	f_dihedral_angle_d	21.9239	774

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 (%)
1.85-1.87	0.3378	140	0.2976	2658	X-RAY DIFFRACTION	99.54
1.87-1.9	0.3512	141	0.2745	2673	X-RAY DIFFRACTION	99.33
1.9-1.93	0.3604	135	0.2795	2567	X-RAY DIFFRACTION	98.54
1.93-1.96	0.2763	140	0.2527	2661	X-RAY DIFFRACTION	99.36
1.96-1.99	0.2968	139	0.2448	2641	X-RAY DIFFRACTION	99.43
1.99-2.02	0.2703	139	0.2531	2640	X-RAY DIFFRACTION	99.43
2.02-2.05	0.2766	138	0.2472	2614	X-RAY DIFFRACTION	98.74
2.05-2.09	0.2814	138	0.2369	2624	X-RAY DIFFRACTION	97.25
2.09-2.13	0.2618	137	0.2134	2598	X-RAY DIFFRACTION	98.59
2.13-2.17	0.2249	140	0.1972	2668	X-RAY DIFFRACTION	99.08
2.17-2.22	0.2425	139	0.1823	2637	X-RAY DIFFRACTION	99.18
2.22-2.27	0.2629	136	0.1948	2589	X-RAY DIFFRACTION	98.55
2.27-2.33	0.238	142	0.1804	2704	X-RAY DIFFRACTION	99.13
2.33-2.39	0.2141	138	0.1795	2609	X-RAY DIFFRACTION	99.21
2.39-2.46	0.2284	139	0.184	2638	X-RAY DIFFRACTION	99.5
2.46-2.54	0.2244	139	0.1816	2647	X-RAY DIFFRACTION	99.08
2.54-2.63	0.2343	140	0.1855	2654	X-RAY DIFFRACTION	99.36
2.63-2.74	0.2525	141	0.1964	2680	X-RAY DIFFRACTION	99.47
2.74-2.86	0.2193	141	0.1794	2676	X-RAY DIFFRACTION	99.82
2.86-3.02	0.2112	139	0.1818	2656	X-RAY DIFFRACTION	99.79
3.02-3.2	0.2026	140	0.1739	2663	X-RAY DIFFRACTION	99.68
3.2-3.45	0.1999	141	0.1719	2668	X-RAY DIFFRACTION	99.33
3.45-3.8	0.1576	139	0.1665	2647	X-RAY DIFFRACTION	98.83
3.8-4.35	0.1839	141	0.1623	2675	X-RAY DIFFRACTION	98.91
4.35-5.48	0.1889	142	0.1736	2690	X-RAY DIFFRACTION	99.44
5.48-45.78	0.1963	143	0.2021	2733	X-RAY DIFFRACTION	99.1

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	3.22054709731	-0.0090498364322	0.318524243889	2.44736435382	-0.172416596384	1.69229609712	0.136900514383	0.397333547527	0.209542553334	-0.290525318435	-0.153563764732	-0.173203422907	-0.0287029827734	0.0825799509271	-0.0032351879334	0.120900770614	0.056911169163	0.0366796465623	0.208561593877	0.0419102531792	0.15323441383	18.1511082941	12.0785015041	44.9883781347
2	3.12218938894	0.0977609923359	0.109312757477	2.16162233068	0.694020187297	0.40227321256	0.194883358373	0.319267219057	0.113354929216	-0.359552630911	-0.208706982907	-0.327050290577	-0.0232403722428	0.0803367692358	0.0387435293926	0.156651841647	0.0616556981539	0.0430431015368	0.235140771684	0.0556215241382	0.166843403249	27.8687979793	1.94859766012	47.5329816776
3	1.53283540267	-0.236284743962	0.643184769253	1.98087378485	0.616693347319	3.27234627141	0.279247133028	0.269057155024	-0.224731958506	-0.30185605271	-0.264573224554	0.171865620162	0.109011503467	-0.116590894365	-0.0189888515173	0.141274963967	0.0753712513447	-0.0331845225238	0.228164633042	-0.0191807248739	0.155615728094	19.574450772	-9.65740659149	47.3267695391
4	3.01353445983	-0.659666325595	1.43227955354	3.74579497312	-1.63901343987	4.9403211347	0.174801160359	0.29949027841	-0.220908017261	-0.426386276195	-0.171132878114	0.102166808007	0.0802576436363	-0.0581043941183	-0.0471919527061	0.141543574726	0.0855746051567	-0.0145642408523	0.235711220714	-0.0920014120477	0.161548313799	3.49716766997	5.26219662408	40.4280183354
5	2.49744595623	0.555231919794	-0.262205028505	2.51240270161	-0.201588311725	2.75243433567	0.20095326164	0.147930860154	-0.271933463186	-0.12454651662	-0.197781592847	0.187568400244	-0.00973831271122	-0.0635603383912	-0.0311523221782	0.100256464131	0.0576924516701	-0.021595660231	0.153751172264	-0.0288305082974	0.181120852486	-0.590310249029	9.38735542741	48.2411006816
6	2.81611692297	-0.68683997644	0.870011366063	2.75960711005	-0.888547771044	2.00213107313	0.116248323927	0.271709453245	-0.800605303468	-0.355685151331	-0.0476087745417	0.636480131013	0.224550631524	-0.229403206373	-0.0155296566675	0.172411115313	0.0183359287364	-0.0928702456707	0.244470548688	-0.101464225426	0.417486944581	-10.1590715073	1.17805080201	45.8547516098
7	3.30110439795	-0.109088639194	-0.292803108973	2.59826160748	-0.813521990936	0.442019607989	0.121612853029	0.336272239703	-0.292596626529	-0.284678954275	-0.0877640844433	0.320526476311	-0.0254613594067	-0.231504559709	-0.0340979176175	0.146435253645	0.0554882586255	-0.0470867631495	0.230178416934	-0.0602094434603	0.16582437613	-10.7908720681	16.7450190442	47.9232324123
8	2.34553286581	0.104804930731	-0.567501814898	2.2355194122	-0.184901253811	2.1740672073	0.329795962439	0.482567863411	0.251360660396	-0.443998788349	-0.265130526244	-0.196872052136	-0.137604434773	0.12247867402	-0.0486658078008	0.171621037402	0.0974878969024	0.0686615669423	0.25646351726	0.0373617512899	0.180171651348	-2.7151913234	28.1670873683	47.0508627072
9	4.44414696799	-0.271678451873	1.8877245784	3.96071977119	-0.636717613807	5.78382418826	-0.0237909649293	-0.457665605033	-0.328358642814	0.639125009815	0.25191717883	0.0847756175769	0.354518901183	0.154997395808	-0.35142684039	0.293522939373	0.0884467224551	0.0688033146767	0.159269381872	-0.00387439871106	0.182653060771	-24.9216842487	17.4954069391	19.4680828538
10	2.51227348765	0.340404916126	0.273830179472	2.98675465326	0.383549630013	2.23141771882	-0.1683795793	-0.196435487157	-0.214329746388	0.327304125061	0.134938595025	0.31893583352	0.0957704826752	-0.121169351954	0.0266744163413	0.180412703613	0.0587813856271	0.05422275101	0.102837750196	0.0255788832422	0.192393310732	-23.584914751	10.2714395249	12.5537403228
11	2.65004853328	0.432196991707	0.755568278701	3.24836295722	0.272063036336	0.532048699946	-0.142235665005	-0.35993745305	-0.336878081198	0.361287757288	0.124620800795	0.0805701763	0.139778765499	-0.0541131120057	0.0245908674791	0.216266808138	0.0593859718258	0.0725639070123	0.148127079201	0.0396339121652	0.169138912623	-13.926986477	2.78660851565	12.4942005848
12	1.77300837108	0.0822766727209	0.979691992527	2.36441554068	1.44502314877	4.81660301457	-0.346903654626	-0.353193798867	0.149705725916	0.454097617244	0.188572874351	0.0299399148685	0.086496627529	0.238916733571	0.168236018525	0.260812636327	0.0941605188805	-0.0137039109412	0.183877663313	-0.0161019166716	0.163895796145	-2.35083742676	8.8209155939	15.8308444914
13	4.20138958724	-0.778222257459	2.79315871296	1.55760884601	-0.721860907926	4.29600493305	-0.195214443794	0.000285569957408	0.258769150864	0.125563204735	0.21075632208	-0.319947491833	-0.214138254111	0.289184124224	-0.0116987843477	0.19162503	0.040607609232	-0.00789807718557	0.111824217851	-0.0244192010998	0.182413110113	-2.10232895065	14.5007310987	7.90175245129
14	2.78945521116	-1.00648389675	-1.78245096272	4.06359257453	4.17791505446	6.37518803753	-0.0656086964827	-0.136126725273	0.361421405321	0.246692915859	0.345887556227	-0.642079034306	-0.00601042143676	0.33287466911	-0.250393105347	0.21215097552	0.0666657628244	-0.0877251667915	0.133599986493	-0.0167081893707	0.267862224154	30.3240635625	-15.4779074489	13.8075438824
15	2.40377620404	0.136780554319	0.179059100177	2.58638696621	-0.46940550653	2.67868838355	-0.240612044211	-0.299289192551	0.143303114091	0.307557224447	0.125463580066	-0.142144956312	-0.0542637561482	-0.0130355131873	0.112341318775	0.190693895098	0.078829712466	-0.0309037329491	0.113887720338	-0.0314621977919	0.185332374345	20.5677919253	-12.1670415876	14.9718158016
16	1.9217772408	-0.682626197688	-1.23359999824	1.72564993043	0.511638228323	1.83278966822	-0.149803628899	-0.313417969003	0.618701106747	0.410132472673	0.327323865562	-0.806800018148	-0.123989717265	0.385395826735	-0.0492497076481	0.262048197392	0.0304316367034	-0.117770576435	0.178659163752	-0.088546346824	0.423156050599	29.6988041838	-1.77232270275	13.7251181596
17	1.03704916533	-0.923195964639	0.198075940616	2.14168736166	-0.885958184299	0.418499363982	-0.219297146114	-1.21408109708	0.267158280131	1.38227829532	0.610575842334	-0.69463337086	-0.25821490649	0.391122668895	-0.186183067001	0.563107119334	0.188051875901	-0.226248160108	0.482257657904	-0.245543234079	0.174369575315	14.7320828063	5.01823755945	18.9895132893
18	3.01528643506	-0.601394179629	-0.0285541209013	2.41009490935	-0.0775615243716	0.992541044336	-0.243068744857	-0.415061492522	-0.0971079649072	0.393830913315	0.248086033661	0.266307964192	0.0211687374436	-0.0602738064368	0.00624321143027	0.220541952959	0.0717114893175	0.0190407698808	0.145539423624	0.0275537814765	0.131128746578	6.39294123411	-6.95838596722	11.611389487

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 98 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 99 through 136 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 137 through 184 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 8 through 36 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 37 through 79 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 80 through 98 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 99 through 136 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 137 through 184 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 8 through 36 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 37 through 98 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 99 through 136 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 137 through 165 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 166 through 184 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 8 through 24 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 25 through 79 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 80 through 98 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 99 through 109 )
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 110 through 184 )

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