PDB-9dcs: Structure of a TelD-associated type VII secretion system DUF4176 ...

ID or keywords:

Entry

Database: PDB / ID: 9dcs

Title

Structure of a TelD-associated type VII secretion system DUF4176 protein

Components

DUF4176 domain-containing protein

Keywords

CHAPERONE / Molecular chaperone / type vii secretion system / antibacterial toxins

Function / homology

ACETIC ACID / FORMIC ACID

Function and homology information

Biological species

Streptococcus intermedius (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.4 Å

Authors

Grebenc, D.W. / Kim, Y. / Whitney, J.C.

Funding support

Canada, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: A widespread family of molecular chaperones promotes the intracellular stability of type VIIb secretion system-exported toxins.
Authors: Gkragkopoulou, P. / Garrett, S.R. / Shah, P.Y. / Grebenc, D.W. / Klein, T.A. / Kim, Y. / Whitney, J.C.

History

Deposition	Aug 27, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 5, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9dcs.cif.gz	210.2 KB	Display	PDBx/mmCIF format
PDB format	pdb9dcs.ent.gz	142.5 KB	Display	PDB format
PDBx/mmJSON format	9dcs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9dcs_validation.pdf.gz	463.5 KB	Display	wwPDB validaton report
Full document	9dcs_full_validation.pdf.gz	466.2 KB	Display
Data in XML	9dcs_validation.xml.gz	16.9 KB	Display
Data in CIF	9dcs_validation.cif.gz	22 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/dc/9dcs ftp://data.pdbj.org/pub/pdb/validation_reports/dc/9dcs	HTTPS FTP

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Related structure data

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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#32 - Aug 2002 Chaperones similarity (1) #4 - Apr 2000 Collagen similarity (1) #116 - Aug 2009 Sulfotransferases similarity (1)

Deposited unit

A: DUF4176 domain-containing protein

B: DUF4176 domain-containing protein

C: DUF4176 domain-containing protein

D: DUF4176 domain-containing protein

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	82.490, 82.490, 144.880
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	152
Space group name H-M	P3₁21
Space group name Hall	P3₁2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+1/3 #3: -x+y,-x,z+2/3 #4: x-y,-y,-z+2/3 #5: -x,-x+y,-z+1/3 #6: y,x,-z

#1: Protein	DUF4176 domain-containing protein Mass: 12222.022 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus intermedius (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-ACY / ACETIC ACID Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.96 Å³/Da / Density % sol: 58.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 1.8305 M Malonic Acid, 0.25 M Ammonium Citrate Tribasic, 0.12 M Succinic Acid, 0.3 M DL-Malic Acid, 0.4 M Sodium Acetate Trihydrate, 0.5 M Sodium Formate, 0.16 M Ammonium Tartrate Dibasic

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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: 0.97902 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 11, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97902 Å / Relative weight: 1
Reflection	Resolution: 2.4→40.01 Å / Num. obs: 23007 / % possible obs: 100 % / Redundancy: 18.6 % / B_iso Wilson estimate: 43.46 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.219 / R_pim(I) all: 0.052 / R_rim(I) all: 0.225 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2.4→2.46 Å / Redundancy: 13.9 % / R_merge(I) obs: 2.825 / Mean I/σ(I) obs: 1 / Num. unique obs: 1676 / CC_1/2: 0.406 / R_pim(I) all: 1.114 / R_rim(I) all: 3.046 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.19_4092	refinement
xia2		data reduction
xia2		data scaling
MLPHARE		phasing
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.4→40.01 Å / Cross valid method: FREE R-VALUE / σ(F): 2.21 / Phase error: 32.8746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2752	1086	4.74 %
R_work	0.2277	21834	-
obs	0.2303	22920	99.79 %

Solvent computation

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

Displacement parameters

B_iso mean: 68.7 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→40.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3167	0	10	21	3198

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0019	3245
X-RAY DIFFRACTION	f_angle_d	0.4471	4390
X-RAY DIFFRACTION	f_chiral_restr	0.0375	468
X-RAY DIFFRACTION	f_plane_restr	0.0036	581
X-RAY DIFFRACTION	f_dihedral_angle_d	14.2333	1176

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 (%)
2.4-2.51	0.3789	148	0.359	2658	X-RAY DIFFRACTION	93.49
2.51-2.64	0.3893	126	0.3125	2689	X-RAY DIFFRACTION	95.29
2.64-2.81	0.3647	116	0.2995	2697	X-RAY DIFFRACTION	95.84
2.81-3.02	0.3063	162	0.2673	2671	X-RAY DIFFRACTION	94.18
3.02-3.33	0.3017	143	0.2497	2708	X-RAY DIFFRACTION	94.98
3.33-3.81	0.2769	108	0.2168	2757	X-RAY DIFFRACTION	96.23
3.81-4.8	0.2174	157	0.1813	2737	X-RAY DIFFRACTION	94.57
4.8-40.01	0.2496	123	0.2114	2920	X-RAY DIFFRACTION	95.93

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	5.44219964673	0.0985273749525	-6.08982839443	4.97514686814	-2.02670132664	7.56198791689	0.646056363053	-0.0846948910427	0.480218517595	0.421715624913	-0.0473875024642	-0.162457741619	-0.557272354829	0.265151295311	0.303278972803	0.822595810963	-0.187593657722	-0.000503566454714	1.000322593	0.0164769703817	0.045974604908	-9.11010049625	52.392886511	25.5916904558
2	3.51821648085	0.881685348909	-2.61295961634	4.06478193931	-0.946996804708	3.91166329391	-0.203179767821	0.154877046543	-0.00785462886503	0.192006265928	0.466515793979	0.383361507659	0.104204866779	-1.22769307471	-0.347509522647	0.747834603602	0.00411977039137	-0.00856243914599	0.674861384333	0.102077237106	0.233778793173	-16.3080827415	44.7414010171	20.8621690439
3	2.20395361464	0.701125491103	2.27580455187	5.42506354622	2.03237584131	3.65776483818	-0.0259743943386	1.05280658106	0.0468628629777	-0.643832607809	0.0179920206803	-0.0561827988577	0.102562799399	-0.118060437115	-0.465443838072	0.782514725122	-0.0543008381867	0.201837290411	0.789327438796	0.142063510895	0.475992977359	-8.62852182535	51.707066063	6.50824057232
4	2.21508428063	-0.857910412446	0.595412175386	3.24140253455	-2.07134050762	3.91967802572	0.26172295456	0.0923694270927	0.106720993345	-1.0735062936	0.0221986019331	-0.377342160661	0.895010166318	-0.592065902549	-0.150646568869	0.726562707742	-0.0557057016171	0.0297938062155	0.915152955181	-0.0820295122624	0.270371824511	-11.2340343296	39.4102742238	17.6242843636
5	1.64062748684	-1.14351749699	0.504780219261	3.38887748873	-0.876636947133	3.65864961356	0.164878005177	0.623451303598	0.519600567105	-0.707700469254	0.163477525613	0.21202782005	-0.133534276271	-0.801125538452	-0.101007671052	0.654365551949	0.385251029748	0.0977474464272	1.1246683754	-0.0302536534939	0.174980010544	-15.449067871	50.1849466718	15.9100437746
6	6.19550843276	-0.496048971665	0.453312195432	1.28413695856	1.21878890392	3.87970846423	-0.162885753035	-0.267247469366	0.363466074517	0.0987265678991	0.0521660833959	0.192003486795	-0.160749369009	-0.633408761726	0.219352513164	0.548147541226	-0.33338213776	-0.0207482988313	0.542008067131	0.0228171190771	0.417898870778	-12.4102640427	48.4971775388	29.4143606149
7	3.48161149292	0.645653549991	-1.19428940992	0.701675266885	-0.609740788483	1.1786363376	-0.378428028958	0.479941262858	0.337299000403	-0.965424635138	0.571523485263	0.501530391012	-1.06359759848	0.0451464588827	0.0941669384488	1.23755255395	0.329095927575	-0.0286332165371	1.02967938635	0.180438913279	0.151006126162	-0.989242525754	58.98697249	23.6850578565
8	2.78763273867	-1.71617179543	-3.03389653866	3.37156631231	0.452751589499	4.43447869044	0.474927583867	-0.265083700797	0.0449394408709	0.0104595687602	0.309813252617	-0.317724461485	-0.755481661546	0.642814726813	-0.282027642034	0.948446584364	-0.0310251541744	-0.0646393477075	1.11812324071	0.175348469361	0.465778059918	-8.79308490327	57.6176537736	7.94490868921
9	8.05844838707	1.33695712759	-3.76768934273	3.07029012676	1.68763058695	3.63317095654	-0.424103863988	0.399057225298	0.335382975813	-0.291049467346	-0.0795325837137	0.515000975212	0.902359822011	0.00108234522321	0.696081392495	0.865991161016	0.20569211636	-0.0936982647605	1.47744750073	0.196577996961	0.499266664692	-20.2864305405	46.66790513	8.27370458061
10	5.17452195419	-0.382838584554	5.05302668357	4.32451656715	3.11228902041	7.76727587619	-0.363118992977	-1.4700166672	-0.354670049468	0.413931705984	0.358363473342	-0.0536142250227	1.40435548846	-0.398800171978	0.452852368274	1.07289402247	0.369196320687	0.147227852736	1.15089174119	-0.284410898971	0.0458464217484	-6.68074385662	33.0307105578	31.896821812
11	1.66658880687	0.799884411411	-0.973349367037	2.44396650265	1.66355361434	6.81926055942	0.149965726019	-0.0354112918628	0.104401537677	-0.101942545244	0.103613436316	-0.389869293166	-0.353045545561	-0.0036173151916	-0.329770745889	0.911967715738	0.118387488722	0.0920804429771	0.713670308855	-0.0521944268717	0.270353289074	3.0478654017	38.4397357258	28.5354945758
12	0.919948665091	-1.89723851924	0.802741139128	4.76985941263	-0.985545493372	1.25005637453	-0.0159486096133	0.691776452638	-0.25832087945	-0.426978928342	-0.613334745016	-0.166427458145	0.583179970586	1.94256896856	-0.0046683182882	1.13083128583	0.12736289954	0.0499305488525	1.23499368258	0.0746166902102	0.452060084856	2.78251867954	24.2553236918	18.8834074542
13	1.75869296581	1.13203230329	1.79717606342	2.62777337537	0.0804955272894	2.45334039026	-0.258386745846	0.268314714475	-0.143227975051	-0.601688440989	0.0634095409794	-0.385589315918	-0.0362823195629	0.407482967563	-0.101376116906	0.862507562281	-0.116991932202	-0.0215337494695	0.945984917109	-0.0298570554388	0.195026000839	1.24656217111	40.9201095802	19.9861292252
14	1.45092123405	-1.49912269927	-1.00995188779	2.01972199362	2.19521865331	3.4916983469	-0.0849520779479	-0.116036009773	0.166289664629	0.111347983021	-0.122914416145	-0.880915236156	0.147161062612	1.04514037295	-0.411441949733	1.08163090166	0.152167347406	0.107161773462	0.825669529579	-0.0461857395099	0.337260516307	4.07675868051	31.0537263283	26.945738654
15	0.634659860369	-0.401541252229	0.715130155385	0.448098477993	0.180548310901	3.444800168	0.240511427916	-0.415954197478	-0.187466127185	0.249289264814	-0.0352359364405	-0.277612424789	0.147598952879	-0.0962275631907	0.60081260403	1.01986184179	-0.292407998593	0.00839901041569	0.726523407954	-0.0825568271644	-0.123226931418	-5.06341848015	38.8558014168	34.4209878757
16	1.50028527461	-0.265528539547	-0.616834663444	2.75368719587	0.558558131066	2.68362159009	-0.23767351862	-0.0514879173528	0.0732397039127	0.393945009134	0.407686499841	-0.200023929665	0.320490938364	0.365912460445	-0.351432034553	0.778553459437	-0.217289063534	0.00569027382342	1.04085207541	0.0112639757978	0.340628959566	-15.0390900079	28.1708765259	30.8125053936
17	3.0094701017	-2.665989551	1.81593915353	2.37691150656	-1.53592258995	9.14535754349	-0.361676632225	0.439368883017	-1.17625435977	-1.21651460141	0.449361824232	0.233061537482	0.843847591735	0.866001479918	-0.0425463046655	1.27135737101	0.173270761971	-0.04445848471	0.658786285644	-0.0607689015411	0.745446848901	4.69651707371	23.4333329363	21.8739795825
18	3.61328176515	1.09887251001	-0.961441757484	2.03175898119	3.21163001334	7.54221296355	-0.055857554954	0.603242057505	0.68488026333	-0.640762444281	0.0311675980063	0.176923005152	-1.6377060703	-0.240233421613	0.0903898020066	0.769158642137	0.0688367993997	-0.0392929684971	0.753806771895	0.0549641814439	0.380761011677	9.03943538042	52.3582350522	-1.51544631458
19	1.41910785814	-0.298278667813	-1.19114795527	2.30039274096	1.64037453038	5.52643728113	-0.106144237695	-0.384478814264	-0.248023317882	0.408700210323	-0.0931182217108	-0.153702666248	0.0573447723031	0.548482331383	-0.00124597174823	0.586206404622	-0.144727985206	-0.0723055203054	1.00957131477	0.0717213602371	0.0406672867622	16.3044649673	44.6175360387	3.27817858022
20	2.80268396429	0.286537071198	-2.20661886343	1.84163085692	1.88556802106	4.48290975706	-0.45191447266	0.0572138908829	-0.768199049259	0.892981728529	-0.139414184516	0.172199816708	-0.479998319401	-0.535722741321	0.4794407576	0.781033407147	-0.152555903553	0.0736468687747	0.998417060728	-0.0563869124383	0.403741283797	6.90010508941	50.6443490149	14.9639732452
21	2.78384058525	-0.18755846344	-2.15332846892	4.45469446797	1.84953606028	6.85519153136	-0.0591882756841	-0.352991148967	-0.0982219540918	1.04852857192	-0.427030049896	-0.776275009318	-0.569399223051	0.695296198709	0.175249548457	0.88603191697	0.0112346243059	-0.11721191074	1.16369641108	0.0460157440653	0.357616095081	10.1228374841	52.8159899366	18.1928623496
22	1.57132572498	0.569375734829	0.976466241171	2.98953633214	1.61491909233	3.54712925455	0.228946245385	-0.215132740014	-0.34023258851	0.510497556768	-0.0636363618446	-0.115329858427	-0.327778088918	0.304085143302	-0.0542446081536	0.706941941145	0.0180107845201	0.0121429212162	0.858195749162	0.0319041005245	0.166826821834	12.8106288581	42.8724109464	7.15394700116
23	3.0174377879	-0.106170720929	-1.56678730588	0.825221832054	0.522042779802	1.08861582106	0.102483852795	0.00513948610665	0.562810927266	-0.437734952179	-0.377542992931	0.0587858005128	-0.325928498339	0.708419923911	-0.122135182431	0.936811707173	-0.43967307387	0.223475724446	0.85322896419	0.0932463855015	-0.227241655666	12.4863173339	48.4970763795	-5.23176913172
24	5.76466391263	-2.30215145662	-1.1101911467	1.74250547247	-1.04314823258	3.01746209069	-0.118576468644	-0.715652022552	1.11787058089	0.477087445608	0.894323268518	-0.365390614301	-1.53156435696	-0.0534854753368	-0.266339737056	1.14737024072	0.26289110984	0.0608913655758	0.912943437517	-0.0386899683482	0.180926160795	0.939178830663	59.1300607396	0.399243652346
25	7.53562649844	2.57513975049	-3.00266155138	3.80267103898	-1.52792893645	8.48284017404	0.233736071365	-0.597252876466	0.307645247451	-0.0231325139367	-0.274655111981	-0.36745072254	-1.4993831037	-0.285528646173	0.129263402178	1.11128148638	-0.0780808875266	-0.0826164981174	0.623346784202	0.0677857820975	0.304450199514	11.3646568661	56.3206912813	15.8494369352
26	5.19951172374	0.422607691076	2.71568666247	5.62104605338	-1.94451270798	5.87392585892	0.21282677733	0.749041964406	-0.458743676592	-0.817846034174	0.237500620214	-0.0127390431698	0.331053973363	-0.760282295402	-0.273220717048	0.477160989561	-0.0485364476249	-0.0634965461525	0.61876315585	-0.0344593988035	0.258043543998	-0.155787110451	36.7067021712	-5.42089218289
27	3.4760840546	0.351717758067	0.779666664312	3.02791870386	-0.597775342318	3.99283548902	0.11030961844	-0.0956729410883	-0.0677640064971	0.376064109225	0.17697907503	0.414910712231	0.685202308186	-0.0853961982896	-0.106114686895	0.741521217641	-0.115179754729	0.029336897998	0.638329939771	0.00924301259864	0.227018714092	-0.750867707501	33.765524123	-0.00548746687199
28	6.89993870903	-3.17497793171	-4.35030645062	2.70673107451	0.0151810556391	5.93372547215	-1.06805408807	0.600270224389	-0.721442043946	0.0604655598012	-0.0402422811386	0.213138334671	1.13022698094	0.342928611284	0.828533180805	0.938156374166	0.0107545678	0.00928018244863	1.04888632195	-0.14325457504	0.358052110855	15.4807984161	28.7367857691	-6.48782753911
29	2.559867009	0.783311955177	-0.0257755603355	3.85413357453	1.36325141478	3.88235735138	-0.146300600271	-0.487523244392	-0.354013402091	-0.585716962972	0.228091347004	-0.250780523644	0.0989591168579	-0.401299608121	-0.0620468301024	1.32451925978	-0.225305367237	0.103656159381	0.987183834537	0.132964194581	0.356770789496	-3.70157317375	22.7762380069	1.38568393836

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 8 )	A	A	1 - 8	1 - 8
2	2	chain 'A' and (resid 9 through 24 )	A	A	9 - 24	9 - 24
3	3	chain 'A' and (resid 25 through 37 )	A	A	25 - 37	25 - 37
4	4	chain 'A' and (resid 38 through 53 )	A	A	38 - 53	38 - 53
5	5	chain 'A' and (resid 54 through 60 )	A	A	54 - 60	54 - 60
6	6	chain 'A' and (resid 61 through 71 )	A	A	61 - 71	61 - 71
7	7	chain 'A' and (resid 72 through 87 )	A	A	72 - 87	72 - 87
8	8	chain 'A' and (resid 88 through 94 )	A	A	88 - 94	88 - 94
9	9	chain 'A' and (resid 95 through 103 )	A	A	95 - 103	95 - 103
10	10	chain 'B' and (resid 1 through 8 )	B	D	1 - 8	1 - 8
11	11	chain 'B' and (resid 9 through 24 )	B	D	9 - 24	9 - 24
12	12	chain 'B' and (resid 25 through 38 )	B	D	25 - 38	25 - 38
13	13	chain 'B' and (resid 39 through 53 )	B	D	39 - 53	39 - 53
14	14	chain 'B' and (resid 54 through 60 )	B	D	54 - 60	54 - 60
15	15	chain 'B' and (resid 61 through 71 )	B	D	61 - 71	61 - 71
16	16	chain 'B' and (resid 72 through 82 )	B	D	72 - 82	72 - 82
17	17	chain 'B' and (resid 83 through 100 )	B	D	83 - 100	83 - 97
18	18	chain 'C' and (resid 1 through 8 )	C	E	1 - 8	1 - 8
19	19	chain 'C' and (resid 9 through 24 )	C	E	9 - 24	9 - 24
20	20	chain 'C' and (resid 25 through 29 )	C	E	25 - 29	25 - 29
21	21	chain 'C' and (resid 30 through 38 )	C	E	30 - 38	30 - 38
22	22	chain 'C' and (resid 39 through 60 )	C	E	39 - 60	39 - 60
23	23	chain 'C' and (resid 61 through 71 )	C	E	61 - 71	61 - 71
24	24	chain 'C' and (resid 72 through 87 )	C	E	72 - 87	72 - 87
25	25	chain 'C' and (resid 88 through 96 )	C	E	88 - 96	88 - 96
26	26	chain 'D' and (resid 1 through 24 )	D	F	1 - 24	1 - 24
27	27	chain 'D' and (resid 25 through 71 )	D	F	25 - 71	25 - 71
28	28	chain 'D' and (resid 72 through 81 )	D	F	72 - 81	72 - 81
29	29	chain 'D' and (resid 82 through 98 )	D	F	82 - 98	82 - 93

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