PDB-9glg: X-ray structure of the Thermus thermophilus Q218E mutant of the P...

ID or keywords:

Entry

Database: PDB / ID: 9glg

Title

X-ray structure of the Thermus thermophilus Q218E 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

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: 1.55 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
Revision 1.1	Jul 9, 2025	Group: Database references / Category: citation / Item: _citation.journal_volume

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9glg.cif.gz	159.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9glg.ent.gz	104.4 KB	Display	PDB format
PDBx/mmJSON format	9glg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9glg_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	9glg_full_validation.pdf.gz	1 MB	Display
Data in XML	9glg_validation.xml.gz	19.9 KB	Display
Data in CIF	9glg_validation.cif.gz	26.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/9glg ftp://data.pdbj.org/pub/pdb/validation_reports/gl/9glg	HTTPS FTP

-
Related structure data

Related structure data	9gl5C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
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)

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

Unit cell

Length a, b, c (Å)	108.099, 108.099, 86.183
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	B-378- 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 (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.: 7 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.98 Å³/Da / Density % sol: 58.7 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.5 M LiSO4 0.1 M NaAc pH 7.0

-
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: 1.55→41.13 Å / Num. obs: 54531 / % possible obs: 99.98 % / Redundancy: 12.78 % / B_iso Wilson estimate: 31.17 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.08074 / R_pim(I) all: 0.02645 / R_rim(I) all: 0.08503 / Net I/σ(I): 12.78
Reflection shell	Resolution: 1.55→1.605 Å / Num. unique obs: 5482 / CC_1/2: 0.594

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
MxCuBE		data collection
autoPROC		data processing
XDS		data reduction
XDS		data scaling
Coot		model building
PHENIX	1.17.1_3660	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→41.13 Å / SU ML: 0.2229 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.9279
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2029	1771	3.25 %
R_work	0.1837	52755	-
obs	0.1844	54526	99.99 %

Solvent computation

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

Displacement parameters

B_iso mean: 42.46 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→41.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2226	0	43	287	2556

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2339
X-RAY DIFFRACTION	f_angle_d	1.1585	3204
X-RAY DIFFRACTION	f_chiral_restr	0.0641	354
X-RAY DIFFRACTION	f_plane_restr	0.0051	400
X-RAY DIFFRACTION	f_dihedral_angle_d	36.0483	316

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 (%)
1.55-1.59	0.4227	138	0.3977	4078	X-RAY DIFFRACTION	99.98
1.59-1.64	0.3456	137	0.3324	4051	X-RAY DIFFRACTION	99.95
1.64-1.69	0.3153	133	0.2844	4035	X-RAY DIFFRACTION	100
1.69-1.75	0.2505	139	0.2483	4065	X-RAY DIFFRACTION	100
1.75-1.82	0.2442	137	0.2152	4063	X-RAY DIFFRACTION	99.98
1.82-1.91	0.267	139	0.2085	4057	X-RAY DIFFRACTION	100
1.91-2.01	0.2457	133	0.2046	4076	X-RAY DIFFRACTION	100
2.01-2.13	0.2513	134	0.2003	4026	X-RAY DIFFRACTION	100
2.13-2.3	0.217	133	0.1849	4110	X-RAY DIFFRACTION	100
2.3-2.53	0.1866	135	0.1816	4025	X-RAY DIFFRACTION	100
2.53-2.89	0.2171	137	0.1952	4050	X-RAY DIFFRACTION	100
2.89-3.64	0.2118	137	0.1813	4078	X-RAY DIFFRACTION	100
3.65-41.13	0.1595	139	0.1545	4041	X-RAY DIFFRACTION	99.93

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	2.98248503681	0.266468470878	-0.0488527111017	5.16622473048	0.696383086262	2.41404442792	0.0520687879002	-0.0522567024796	-0.209712963484	-0.084970657989	-0.10256326157	0.674381544063	0.274465452578	-0.499356940125	0.0144694764949	0.288700910746	-0.0511298086347	-0.042512654254	0.381984436583	0.0477176232081	0.366715646774	-26.3401032963	18.4549378568	-8.72294312803
2	5.10503322271	0.190062579182	1.44521544335	4.95250207265	-0.593395784825	3.17079798573	0.152086918495	-0.32758159504	0.0445770961111	0.412709871565	-0.123106898463	-0.205054020688	0.15893115045	-0.0413182162752	0.00330028377626	0.326550926717	0.0048821452195	-0.0168002631642	0.273957425351	0.0250541712036	0.292061958442	-13.5546707846	21.0944361935	-3.44609754881
3	5.84640330589	-0.493418207104	-0.233413951608	4.26026705956	-0.610937981158	3.41870395592	-0.068858183031	0.145791997174	0.0646002874368	-0.179580914418	0.0751471023786	-0.323727822911	0.0271664377949	0.042051501528	0.00108715007092	0.276738023666	0.0229790606097	-0.0223586105167	0.196073031128	0.00936771068432	0.243890268286	0.185813982646	14.8920316711	-5.62087096132
4	3.43912941025	-1.42652820184	0.710706717951	6.20506676982	-0.431529484208	2.49228348237	0.099848271323	0.568637746895	0.143140486782	-0.844226983785	-0.0362059320168	0.688470470834	-0.158205399713	-0.27562825673	-0.0721959476416	0.385792897841	0.0552546305362	-0.0675657893641	0.356964387827	0.0634485312833	0.324979590434	-23.629782629	37.5629713682	-11.8891344797
5	3.29158274687	2.48473311042	1.36017460138	7.55294935636	3.42837952434	4.87748833219	0.21836691898	-0.229294322773	0.604572677768	0.40449527189	-0.43406117607	1.18081298466	-0.317238893672	-0.368870245586	0.209611914111	0.336318326623	0.100652645652	0.0954140815359	0.431697379181	0.0474018327261	0.645539800499	-30.2013399825	43.060233807	-1.87946888475
6	1.49675074017	0.0409426493448	0.63122700927	7.37247396111	0.334624104919	2.01636316618	-0.00541881892535	-0.326200721377	0.198642119008	0.437420248668	0.0161402875903	0.492280493747	-0.269440041018	-0.130343685198	-0.106299438927	0.353410192359	0.0122752415928	0.0612752916621	0.340397781028	0.0262130122698	0.312110027455	-21.0499684856	40.1542307562	0.649612347985
7	5.22903033924	0.478952335145	-0.035017067578	3.94728660363	-0.0510357407301	2.81700151757	0.281804065256	0.293127282271	0.128515588101	-0.0887731290668	-0.073003211161	-0.0352793907698	0.0488721042469	-0.0310823847243	-0.231531875388	0.353262950647	-0.0165750962911	0.0471643229898	0.274216665574	-0.00272462342102	0.284442533416	-11.6201647251	39.8364109738	-10.1432471691
8	3.22272063232	-0.30877676284	0.598835674659	1.71080704131	-0.732550407887	3.77453819891	-0.0473162815813	-0.15404967301	0.00717590156734	-0.24926331636	-0.0404719493256	-0.577693432624	-0.034144043016	0.465949871116	0.106665759369	0.369920043001	-0.0078931884232	0.0353562350275	0.314680373134	0.0279145445218	0.427804979608	4.89210637749	47.6868857056	-5.22632985726
9	3.21449275424	0.205324101281	-1.02942964047	1.93816273377	-1.18360778673	3.42857138373	-0.162138438283	0.234188966245	-0.230926919055	-0.432925456935	-0.00643738581874	-0.342056087834	0.38243095691	0.0258956899559	0.197610625856	0.443434504221	-0.00484912427413	0.1341478716	0.272771518171	0.0269245686684	0.365641268931	2.14253453743	46.6445254398	-12.4514160785
10	3.73425838777	4.12982161547	-3.84159443259	6.60471926198	-3.10210738534	4.8598408772	0.470436469819	0.731897898061	1.31503954329	-0.283809336625	0.126160636432	0.92752984992	-0.608011949627	-0.347899050661	-0.632423661915	0.392015139682	-0.000443398119495	0.0577594041922	0.28191879787	0.046893612232	0.426571852413	-6.21566198518	54.2477613676	-10.0127492892
11	3.69652699812	0.918592939343	0.438044833467	3.35174765833	-1.05321359015	2.80905584162	-0.0601633138657	-0.305595222004	-0.197722226972	0.187887073288	-0.15600436782	-0.413102786566	0.287999972351	0.230692075569	0.223577753721	0.39200885974	0.00733274813864	0.0455555958187	0.274219377341	0.0202054417006	0.326318864736	1.48220731729	45.2130733147	-5.39920783446

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 165 through 207 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 208 through 224 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 225 through 301 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 165 through 178 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 179 through 193 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 194 through 207 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 208 through 224 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 225 through 248 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 249 through 266 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 267 through 277 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 278 through 301 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi