PDB-8ssk: Citrobacter rodentium contact dependent growth inhibition (CDI) e...

ID or keywords:

Entry

Database: PDB / ID: 8ssk

Title

Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains

Components

Contact-dependent inhibitor A

Keywords

TOXIN / Peptidase

Function / homology

Function and homology information

catalytic activity / toxin activity / cytoplasm
Similarity search - Function

Biological species

Citrobacter rodentium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Cuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Citrobacter rodentium contact dependent growth inhibition (CDI) entry and toxin (CdiA-CT) domains
Authors: Cuthbert, B.J. / Goulding, C.W. / Hayes, C.S. / Nhan, D.Q.

History

Deposition	May 8, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 15, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ssk.cif.gz	815 KB	Display	PDBx/mmCIF format
PDB format	pdb8ssk.ent.gz	562.7 KB	Display	PDB format
PDBx/mmJSON format	8ssk.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ssk_validation.pdf.gz	506.3 KB	Display	wwPDB validaton report
Full document	8ssk_full_validation.pdf.gz	518 KB	Display
Data in XML	8ssk_validation.xml.gz	58.5 KB	Display
Data in CIF	8ssk_validation.cif.gz	86.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/8ssk ftp://data.pdbj.org/pub/pdb/validation_reports/ss/8ssk	HTTPS FTP

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Related structure data

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	#55 - Jul 2004 DNA Ligase similarity (2) #150 - Jun 2012 Sliding Clamps similarity (2)

Deposited unit

A: Contact-dependent inhibitor A

B: Contact-dependent inhibitor A

C: Contact-dependent inhibitor A

D: Contact-dependent inhibitor A

hetero molecules

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

1

A: Contact-dependent inhibitor A

hetero molecules

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

2

B: Contact-dependent inhibitor A

hetero molecules

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

3

C: Contact-dependent inhibitor A

hetero molecules

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

4

D: Contact-dependent inhibitor A

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.870, 113.982, 87.351
Angle α, β, γ (deg.)	90.000, 92.390, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Contact-dependent inhibitor A / CdiA-PT/CT Mass: 33576.453 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Citrobacter rodentium (bacteria) / Gene: stbD, E2R62_11320 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A482PFX0

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Non-polymers , 5 types, 1283 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1250 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.48 Å³/Da / Density % sol: 50.33 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M sodium acetate, pH 4, 2 M ammonium sulfate

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→39.26 Å / Num. obs: 101283 / % possible obs: 98.5 % / Redundancy: 7 % / B_iso Wilson estimate: 22.87 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.118 / R_pim(I) all: 0.074 / R_rim(I) all: 0.14 / Χ²: 0.98 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 7 % / R_merge(I) obs: 1.187 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4996 / CC_1/2: 0.746 / R_pim(I) all: 0.748 / R_rim(I) all: 1.409 / Χ²: 0.99 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→39.26 Å / SU ML: 0.1788 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.3018
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.186	10055	9.94 %
R_work	0.1618	91125	-
obs	0.1642	101180	98.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 28.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→39.26 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8807	0	146	1253	10206

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0069	9236
X-RAY DIFFRACTION	f_angle_d	0.916	12551
X-RAY DIFFRACTION	f_chiral_restr	0.0534	1384
X-RAY DIFFRACTION	f_plane_restr	0.0073	1645
X-RAY DIFFRACTION	f_dihedral_angle_d	6.3118	1329

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 (%)
1.9-1.92	0.3046	332	0.2673	3007	X-RAY DIFFRACTION	98.09
1.92-1.94	0.2839	327	0.2447	3028	X-RAY DIFFRACTION	98.59
1.94-1.97	0.266	346	0.2367	3073	X-RAY DIFFRACTION	98.84
1.97-1.99	0.2516	331	0.221	2992	X-RAY DIFFRACTION	98.43
1.99-2.02	0.2628	338	0.2154	3018	X-RAY DIFFRACTION	98.21
2.02-2.05	0.2418	323	0.2089	3035	X-RAY DIFFRACTION	98.3
2.05-2.08	0.2392	327	0.2089	3009	X-RAY DIFFRACTION	96.78
2.08-2.11	0.2415	334	0.1968	2890	X-RAY DIFFRACTION	95.02
2.11-2.14	0.2166	336	0.1861	3058	X-RAY DIFFRACTION	99.09
2.14-2.17	0.2188	339	0.1817	3075	X-RAY DIFFRACTION	99.56
2.17-2.21	0.1988	325	0.1709	3064	X-RAY DIFFRACTION	99.5
2.21-2.25	0.1965	332	0.171	3068	X-RAY DIFFRACTION	99.24
2.25-2.3	0.1794	356	0.1583	3030	X-RAY DIFFRACTION	98.92
2.3-2.34	0.1945	326	0.152	3046	X-RAY DIFFRACTION	98.68
2.34-2.39	0.1926	331	0.1603	3072	X-RAY DIFFRACTION	98.52
2.39-2.45	0.2103	332	0.158	3007	X-RAY DIFFRACTION	98.18
2.45-2.51	0.1961	333	0.1614	2971	X-RAY DIFFRACTION	97.18
2.51-2.58	0.2123	330	0.1621	3010	X-RAY DIFFRACTION	96.45
2.58-2.65	0.1855	342	0.1593	3056	X-RAY DIFFRACTION	99.3
2.65-2.74	0.1973	338	0.1577	3040	X-RAY DIFFRACTION	99.29
2.74-2.84	0.1772	336	0.1544	3066	X-RAY DIFFRACTION	99.21
2.84-2.95	0.1709	331	0.1551	3074	X-RAY DIFFRACTION	99.27
2.95-3.09	0.1968	345	0.161	3055	X-RAY DIFFRACTION	98.89
3.09-3.25	0.188	339	0.1546	2995	X-RAY DIFFRACTION	97.69
3.25-3.45	0.1525	333	0.1451	3011	X-RAY DIFFRACTION	96.96
3.45-3.72	0.1569	340	0.1388	3102	X-RAY DIFFRACTION	99.65
3.72-4.09	0.1349	336	0.1248	3058	X-RAY DIFFRACTION	99.04
4.09-4.68	0.1278	340	0.1222	3074	X-RAY DIFFRACTION	98.56
4.68-5.9	0.1795	339	0.1544	3047	X-RAY DIFFRACTION	97.95
5.9-39.26	0.1939	338	0.1879	3094	X-RAY DIFFRACTION	97.5

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	6.02290625369	1.50781407234	-6.13112760736	0.701829334706	-1.31188414418	6.39736389033	0.184279675599	-0.141651021014	0.123010923599	0.139586797284	-0.0737623649734	-0.282871811382	-0.283513405416	1.17022415949	-0.111872397468	0.234552925552	-0.0599792048426	-0.0449465535143	0.52577571402	-0.00883385886271	0.226166568659	-5.6069129972	10.4412505115	-11.4561944295
2	3.31414360781	0.650632636004	-0.0642653486024	0.832666138946	0.825276446832	5.22587950504	0.0140539360757	-0.383437639909	0.0376985769517	0.167924391288	-0.0175509076681	-0.155194553438	-0.184765984989	0.962777410181	0.00145208568657	0.210663396317	-0.0230303438667	-0.0219184168685	0.32016384232	0.00897652251184	0.163365373627	-5.4776311373	12.0376528137	-30.6687049742
3	3.0016773374	1.86700734785	-0.468101193209	2.65285412697	-0.00141915269845	0.78246566762	0.253037124684	-0.282086395646	0.238471099833	0.464326574569	-0.162155122351	0.488010381986	-0.0297584271516	-0.185932302233	-0.0961157441689	0.271186459587	0.0169601549511	0.0871935410733	0.170302901164	0.013502471203	0.257097866052	-28.1433485511	-2.84567045722	-35.6927160614
4	2.35584682059	0.121053156686	-0.936545035664	2.8707669926	-0.613712448951	2.5645467634	-0.0332826045871	-0.143107403185	-0.142969964787	0.131202314471	0.0084922655937	-0.085389479081	0.122913221494	0.14163887611	0.018447040489	0.119663588847	-0.0010205266547	-0.0183661724609	0.0814015193629	0.0131949110455	0.109814088786	-15.0290801841	-10.2788736637	-49.6416359457
5	6.85328361441	-1.27590248461	-7.35585520699	0.801266769827	0.810602752517	8.46185332107	0.140060864123	0.0782754206942	0.235293024207	-0.0522302719513	-0.0397792937822	0.254297981961	-0.203987975804	-1.08099895771	-0.100545723083	0.207592139328	0.0367434204804	-0.0360714759316	0.450221404682	-0.0192810666275	0.183545006299	-28.3601216972	9.85322166583	-32.6850673516
6	4.50198872842	-0.374563681864	-0.0251653241749	2.22742087978	-0.262789644627	5.29198583629	0.0373783093276	0.241629146094	0.0535180467536	-0.0865192464567	-0.026173722129	0.190641129032	-0.132210591219	-0.800489015938	-0.012865856131	0.175226179065	0.0367776938286	-0.0092068419069	0.266026609212	0.00321716269175	0.134287724873	-28.588935887	11.6240252135	-13.6314354579
7	6.98658118487	-4.70315229106	1.54161659387	3.16484805488	-1.03991258219	0.338759038967	0.222379264554	0.386904753236	0.493802869958	-0.270490407846	-0.293240330585	-0.497080308368	0.0514188179927	-0.0449238793062	0.0732589348957	0.503468134088	-0.0092921257135	0.0884825072628	0.319394311164	0.00922790180184	0.326853847402	-1.31295714485	-2.53509154138	-11.3512320587
8	2.37617629274	-0.370646418321	-0.813315371256	3.0776278732	0.530384229848	3.12423236828	-0.00212552567027	0.162425003425	-0.12050746015	-0.205750993229	0.00639005133307	-0.0166630382473	0.105868877173	-0.0350005635383	-0.00837011987909	0.107860337261	0.0148627161622	-0.00654192695003	0.108223185253	-0.0195492197515	0.103318522934	-17.4403476645	-8.71587723085	4.72957708981
9	8.69235172547	2.30162219667	-3.46358071888	0.713025890585	-0.945777221392	1.55915744339	0.075891721283	-0.737378623379	-0.222181203367	0.227417305488	-0.184433673801	-0.0486357697477	0.153915001981	0.124876873885	0.108892184048	0.200413039222	-0.0281184883954	-0.0107330596783	0.247885024249	0.000217994325415	0.153175917078	-12.3164734908	-44.576730259	-6.22266177299
10	4.63564533781	-0.282659682466	0.408539455589	2.8342862162	0.423054519623	3.80800460198	0.0096122928585	-0.401426864685	0.0371338214072	0.217528831391	-0.0212170494125	-0.163984375892	-0.0406128761799	0.116396679874	0.000541990452711	0.122813271183	-0.0205787305725	-0.00296089735532	0.140040025785	0.0123185010222	0.117024686739	-28.2645948887	-47.1577772278	-15.6352621437
11	2.55639675943	-0.190222292623	-0.431781761719	2.34479448259	-0.342568260989	2.00640465542	-0.0378450991183	0.0663070004834	-0.148073227614	-0.0988334195904	-0.0270473924265	-0.183371343296	0.0861444227048	0.201534072032	0.0633908420323	0.144381094571	-0.00771825508387	0.00990019651474	0.0854534105932	-0.0130744395374	0.138518774758	-31.4792699104	-34.0154128221	-37.2949206718
12	3.53076499633	-0.333115121873	-1.05747913764	3.52357862135	0.255832857701	2.3479230596	0.0592649226472	-0.0746970482555	0.184303376302	0.0715411632944	-0.0129685079256	0.248707969439	-0.169290277331	-0.00970265535862	-0.0356454982034	0.143863739893	-0.0125333548883	0.00930915287453	0.0669256306085	0.00538037416736	0.148291657851	-39.3739106311	-25.365804075	-34.3404107231
13	2.00458741164	-1.09650396136	-3.39786614034	0.633441685534	0.520685845025	1.58931022759	-0.0321231510155	0.902041813225	-0.327580224198	-0.25091943568	-0.132925073163	-0.0759626675011	0.174030546683	0.0162463890399	0.183368840753	0.202163778769	0.0347640512614	0.00368784433786	0.365297338898	0.0219585623021	0.195902698997	-18.3540725127	-46.7261514487	-37.0032321127
14	2.0117290921	-0.232157338947	-2.58739078456	5.886573118	-1.51521622436	4.52634576751	0.138087823376	0.173972844471	0.0846435225231	-0.143886156111	-0.0481263493195	0.222759026105	-0.137270904097	0.116135562658	-0.110637042451	0.140634053771	-0.00970547225631	-0.0629449353063	0.24974535787	-0.0523680106918	0.196035356733	-6.1754469211	-47.4569251779	-31.170720509
15	1.88370535273	-0.676323119432	-0.855847689166	2.32569353061	1.65569798003	3.69953114997	0.0559299032223	-0.000215077190126	0.144047218443	0.0861809743959	0.0810751965315	0.0323701961064	-0.191693041443	0.162112650679	-0.124644153406	0.125166737112	-0.0105269276688	-0.0132102680335	0.148293677554	0.0183656502789	0.175512316056	-2.56716534822	-43.3827489123	-20.6881774954
16	3.10904635232	0.496883798252	-0.600807388108	3.91806453957	0.042647470683	2.42658487543	0.0260529906765	0.084107245789	0.176244470675	-0.0970044378927	0.0850496360752	-0.140188716588	-0.136473873775	0.00156758244445	-0.1034886096	0.120119249636	0.0234056496645	0.0161098911383	0.0996149551847	-0.00528512942751	0.113413545544	8.08149719048	-25.4843247133	-9.07323255148

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 14 through 47 )	A	A	14 - 47	1 - 34
2	2	chain 'A' and (resid 48 through 150 )	A	A	48 - 150	35 - 137
3	3	chain 'A' and (resid 151 through 187 )	A	A	151 - 187	138 - 173
4	4	chain 'A' and (resid 188 through 318 )	A	A	188 - 318	174 - 304
5	5	chain 'B' and (resid 12 through 47 )	B	G	12 - 47	1 - 36
6	6	chain 'B' and (resid 48 through 150 )	B	G	48 - 150	37 - 139
7	7	chain 'B' and (resid 151 through 172 )	B	G	151 - 172	140 - 159
8	8	chain 'B' and (resid 173 through 318 )	B	G	173 - 318	160 - 305
9	9	chain 'C' and (resid 14 through 47 )	C	N	14 - 47	1 - 34
10	10	chain 'C' and (resid 48 through 150 )	C	N	48 - 150	35 - 137
11	11	chain 'C' and (resid 151 through 212 )	C	N	151 - 212	138 - 199
12	12	chain 'C' and (resid 213 through 318 )	C	N	213 - 318	200 - 305
13	13	chain 'D' and (resid 13 through 47 )	D	Z	13 - 47	2 - 36
14	14	chain 'D' and (resid 48 through 89 )	D	Z	48 - 89	37 - 78
15	15	chain 'D' and (resid 90 through 171 )	D	Z	90 - 171	79 - 159
16	16	chain 'D' and (resid 172 through 318 )	D	Z	172 - 318	160 - 306

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1283 molecules

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Experiment

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Sample preparation

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Structure viewers

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Open data

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Download

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Validation report

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Assembly

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Components

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1283 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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

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Yorodumi