PDB-9gl5: X-ray structure of the Thermus thermophilus Q190E mutant of the P...

ID or keywords:

Entry

Database: PDB / ID: 9gl5

Title

X-ray structure of the Thermus thermophilus Q190E mutant of the PilF-GSPIIB domain in the c-di-GMP bound state

Components

ATP-binding motif-containing protein pilF

Keywords

MOTOR PROTEIN / GSPII / c-di-GMP / ligand binding / c-di-GMP binding Protein

Function / homology

Function and homology information

ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function

Biological species

Thermus thermophilus HB27 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Neissner, K. / Woehnert, J.

Funding support

Germany, 1items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Protonated Glutamate and Aspartate Side Chains Can Recognize Phosphodiester Groups via Strong and Short Hydrogen Bonds in Biomacromolecular Complexes.
Authors: Neissner, K. / Duchardt-Ferner, E. / Wiedemann, C. / Kraus, J. / Hellmich, U.A. / Wohnert, J.

History

Deposition	Aug 27, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 25, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gl5.cif.gz	153.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9gl5.ent.gz	100.2 KB	Display	PDB format
PDBx/mmJSON format	9gl5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/9gl5 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9gl5	HTTPS FTP

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Related structure data

Related structure data	9glgC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#211 - Jul 2017 Pilus Machine similarity (6) #130 - Oct 2010 Riboswitches similarity (1) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: ATP-binding motif-containing protein pilF

B: ATP-binding motif-containing protein pilF

hetero molecules

34.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: ATP-binding motif-containing protein pilF

hetero molecules

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

2

B: ATP-binding motif-containing protein pilF

hetero molecules

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

Unit cell

Length a, b, c (Å)	107.966, 107.966, 86.366
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	146
Space group name H-M	H3
Space group name Hall	R3
Symmetry operation	#1: x,y,z #2: -y,x-y,z #3: -x+y,-x,z #4: x+1/3,y+2/3,z+2/3 #5: -y+1/3,x-y+2/3,z+2/3 #6: -x+y+1/3,-x+2/3,z+2/3 #7: x+2/3,y+1/3,z+1/3 #8: -y+2/3,x-y+1/3,z+1/3 #9: -x+y+2/3,-x+1/3,z+1/3

Components on special symmetry positions

ID	Model	Components
1	1	A-528- HOH
2	1	B-531- HOH

#1: Protein	ATP-binding motif-containing protein pilF Mass: 16270.546 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: pilF, TT_C1622 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q72H73
#2: Chemical	ChemComp-C2E / 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) / c-di-GMP / Cyclic diguanosine monophosphate Mass: 690.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₄N₁₀O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₄O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.68 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6M LiSO4 0.1 M Sodiumacetate pH 7.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.976 Å / Relative weight: 1
Reflection	Resolution: 1.9→32.71 Å / Num. obs: 29580 / % possible obs: 99.97 % / Redundancy: 10.4 % / B_iso Wilson estimate: 44.9 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.1055 / R_pim(I) all: 0.034 / R_rim(I) all: 0.1109 / Net I/σ(I): 10.12
Reflection shell	Resolution: 1.9→1.968 Å / Num. unique obs: 2977 / CC_1/2: 0.636

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Processing

Software

Name	Version	Classification
MxCuBE		data collection
autoPROC		data processing
PHENIX		phasing
autoPROC		data scaling
Coot		model building
PHENIX	v1.17.1-3660	refinement
XDS		data scaling
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→32.71 Å / SU ML: 0.3132 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 31.0064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2251	3243	5.49 %
R_work	0.1926	55879	-
obs	0.1944	29574	99.94 %

Solvent computation

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

Displacement parameters

B_iso mean: 58.77 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→32.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2208	0	46	122	2376

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0064	2296
X-RAY DIFFRACTION	f_angle_d	1.0642	3139
X-RAY DIFFRACTION	f_chiral_restr	0.0529	350
X-RAY DIFFRACTION	f_plane_restr	0.0055	389
X-RAY DIFFRACTION	f_dihedral_angle_d	38.1582	306

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 (%)
1.9-1.93	0.5083	144	0.4854	2396	X-RAY DIFFRACTION	99.37
1.93-1.96		147		2450	X-RAY DIFFRACTION	99.81
1.96-1.99	0.4291	134	0.3836	2382	X-RAY DIFFRACTION	100
1.99-2.02	0.384	148	0.3624	2460	X-RAY DIFFRACTION	100
2.03-2.06	0.3727	144	0.3621	2413	X-RAY DIFFRACTION	99.96
2.06-2.1	0.3421	138	0.3152	2440	X-RAY DIFFRACTION	100
2.1-2.14	0.3673	138	0.3027	2439	X-RAY DIFFRACTION	99.88
2.14-2.19	0.3214	142	0.2786	2406	X-RAY DIFFRACTION	100
2.19-2.24	0.295	142	0.2535	2446	X-RAY DIFFRACTION	100
2.24-2.3	0.3293	148	0.2232	2482	X-RAY DIFFRACTION	100
2.3-2.36	0.2663	138	0.2153	2404	X-RAY DIFFRACTION	100
2.36-2.43	0.2383	140	0.2019	2416	X-RAY DIFFRACTION	100
2.43-2.51	0.2484	142	0.2025	2431	X-RAY DIFFRACTION	99.96
2.51-2.6	0.25	134	0.1969	2380	X-RAY DIFFRACTION	99.92
2.6-2.7	0.2258	148	0.1986	2474	X-RAY DIFFRACTION	99.92
2.7-2.82	0.3071	134	0.2067	2410	X-RAY DIFFRACTION	99.92
2.82-2.97	0.2568	132	0.2134	2457	X-RAY DIFFRACTION	99.96
2.97-3.16	0.2751	140	0.2086	2418	X-RAY DIFFRACTION	99.92
3.16-3.4	0.2323	140	0.2055	2429	X-RAY DIFFRACTION	99.96
3.4-3.74	0.2138	142	0.1772	2444	X-RAY DIFFRACTION	100
3.75-4.28	0.189	134	0.148	2454	X-RAY DIFFRACTION	100
4.29-5.4	0.1733	144	0.1409	2424	X-RAY DIFFRACTION	100
5.4-32.71	0.1559	150	0.1646	2424	X-RAY DIFFRACTION	99.92

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	5.51119689245	-1.7217936585	1.4972612902	4.42166604858	-0.46496991857	2.80732838122	-0.277935017894	0.00901229574682	0.822563468168	0.303664468261	0.1953109103	-0.626924561635	-0.598833073992	0.614166871992	0.0472295366303	0.542430599832	-0.0800861887363	0.0553087451556	0.570563460684	-0.08941746819	0.606811281165	-3.14296628218	32.2298539035	9.25405516566
2	5.27335300058	0.811837362975	1.21721071023	5.79789280279	1.73945775422	3.77449842865	-0.0208752770767	0.671695175212	-0.0939526084219	-0.30674115079	0.117995790996	-0.0718963175369	-0.0930656887932	0.416983039587	-0.00669102440633	0.488054732735	0.0492590187838	0.0305349146188	0.527178442992	-0.00975124693751	0.493776184806	-11.5340583682	22.2602154438	3.67760898667
3	3.34614156418	2.26546015264	-0.199980214114	3.03832189728	0.649463195267	3.36892841078	0.07536663727	-0.121617736519	-0.673643163998	0.231440454392	0.00862995846711	0.242347510356	0.359224163952	0.0344222696146	-0.0254647688455	0.460615503897	0.0344611331016	0.0393213862989	0.49613865003	0.0678689550968	0.630139375362	-14.687189178	4.2336466417	7.89545237721
4	3.54309520633	-0.831899154418	-1.47165094919	3.84398087529	1.54177186077	2.76182409458	0.042353775461	0.331752062261	0.148845664279	-0.535758384799	-0.208378628112	0.383221108784	-0.319505192255	-0.419343341166	0.0961965754135	0.473778480958	0.0485852427521	-0.0397224952078	0.524672768322	-0.103404858439	0.483952254568	-14.0299434874	7.36407637508	0.584015747359
5	3.0698361574	2.3993745462	1.76269218288	5.14467212946	6.38035172189	8.63253131914	0.129388230631	-0.189159867424	-0.259539508247	-0.160454137806	1.05828735032	-1.9536960881	-0.358888744539	0.592464384647	-1.20485222217	0.425995613805	-0.00180960378274	0.0469673161934	0.487411430038	-0.0619602159935	0.604532485691	-3.03959288194	9.72261084004	2.83503480386
6	2.86208962364	0.770476908035	-1.64663473347	5.92966794637	2.0351924785	4.28207872693	-0.106869457506	-0.250462965899	-0.131126554196	-0.0449841908991	-0.182251720455	0.380784552151	-0.249465834715	-0.279030361789	0.130519525141	0.443023753395	0.0598424220471	-0.0121641487278	0.417962418809	-0.0132261856883	0.428737168297	-11.1504598756	9.70542541884	-0.283300489833
7	4.58679590565	1.12920349553	-0.224711194119	7.81706646593	-0.194109184615	2.47965027701	-0.364840016921	-1.08300116792	0.0645610543456	1.56241139891	0.388726003705	0.898891028863	-0.126362210611	0.0403300295709	-0.00899974747855	0.623190240596	0.0902274662975	0.0878000981073	0.681382785349	0.0121385114992	0.562987856343	-17.233963938	7.96354933736	13.9533428993
8	4.99881394722	0.857607995759	-0.920151199047	5.20011256525	0.278683416789	3.03528745227	0.170445772966	-0.00927372211776	-0.236378887675	-0.0838293363451	-0.129580855668	1.08013054392	0.295069983124	-0.390319796813	-0.0276890544914	0.505287712169	-0.0892479305653	-0.0453194864734	0.544248335888	0.0708095838546	0.522629770429	-24.3479491646	22.2121159703	-24.3175961712
9	5.04471339668	-0.825631655808	-0.700098500035	4.47160198523	0.291537732136	3.08048816167	0.0547864782938	0.0527636387641	0.309552205517	0.240157760575	-0.0237702147515	-0.245878817979	-0.0997914361073	-0.068020105812	-0.089384843255	0.583844005295	-0.0120805719629	-0.0674549455187	0.44931290145	0.00780735879662	0.628654405962	-11.25434947	22.4871431415	-18.9006363289
10	4.84277308572	0.956822801698	-0.132385004594	2.01946346946	-1.39794744862	4.93522324023	-0.141637008979	0.304753865223	0.176430848971	0.0894468988067	-0.243669674945	-0.635622521831	-0.0996040548097	0.346112706602	0.401584491589	0.560072037537	-0.0178802194553	-0.0557068056392	0.445417948756	0.0674583450515	0.666990381732	5.03748519794	14.961998702	-21.8206977926
11	2.96960406267	-0.93435444474	1.8101046718	1.95412979961	-1.06296261798	2.30227474901	-0.114927235897	-0.244372655125	0.0274250748247	0.401599619021	0.139686689758	0.284197077012	-0.138151446013	-0.280709043909	-0.00423336095027	0.61721407443	0.0189852516294	-0.0860419935236	0.411382108097	0.0443303974087	0.548697193155	-3.19284199188	11.5850639127	-17.1131555824
12	4.86469714627	0.5177088517	-0.815985282103	3.21456572418	-0.743820786043	3.58560428446	-0.241468916922	0.409070966405	0.173602212443	-0.234091975273	-0.124081134328	-0.304775658462	-0.475953193197	0.110889315567	0.350198911492	0.584663445577	-0.0299142950674	-0.0612018982922	0.422676588995	0.0567248306349	0.517827500565	1.92984995504	17.1019393883	-23.3825719185

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 51 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 68 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 69 through 92 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 93 through 110 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 111 through 121 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 122 through 131 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 132 through 145 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 9 through 51 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 52 through 68 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 69 through 100 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 101 through 121 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 122 through 145 )

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