PDB-2yo3: Salmonella enterica SadA 1185-1386 fused to GCN4 adaptors (SadAK14)

ID or keywords:

Entry

Database: PDB / ID: 2yo3

Title

Salmonella enterica SadA 1185-1386 fused to GCN4 adaptors (SadAK14)

Components

GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

Keywords

MEMBRANE PROTEIN / HANS MOTIF / YADA-LIKE HEAD / YLHEAD / HEAD INSERT MOTIF / HIM / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / CHIMERA

Function / homology

Function and homology information

nitrogen catabolite activation of transcription from RNA polymerase II promoter / FCERI mediated MAPK activation / protein localization to nuclear periphery / Activation of the AP-1 family of transcription factors / response to amino acid starvation / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / mediator complex binding / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Hartmann, M.D. / Hernandez Alvarez, B. / Lupas, A.N.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Complete Fiber Structures of Complex Trimeric Autotransporter Adhesins Conserved in Enterobacteria.
Authors: Hartmann, M.D. / Grin, I. / Dunin-Horkawicz, S. / Deiss, S. / Linke, D. / Lupas, A.N. / Hernandez Alvarez, B.

History

Deposition	Oct 20, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 12, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 9, 2013	Group: Database references
Revision 1.2	Mar 20, 2013	Group: Refinement description
Revision 1.3	Mar 15, 2017	Group: Source and taxonomy
Revision 1.4	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2yo3.cif.gz	319.7 KB	Display	PDBx/mmCIF format
PDB format	pdb2yo3.ent.gz	262.4 KB	Display	PDB format
PDBx/mmJSON format	2yo3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2yo3_validation.pdf.gz	451.1 KB	Display	wwPDB validaton report
Full document	2yo3_full_validation.pdf.gz	456.5 KB	Display
Data in XML	2yo3_validation.xml.gz	33.7 KB	Display
Data in CIF	2yo3_validation.cif.gz	49.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yo/2yo3 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/2yo3	HTTPS FTP

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Related structure data

Related structure data	2ynyC 2ynzC 2yo0C 2yo1C 2yo2C 1gcmS 1ce9 1dgc 1fav 1fmh 1gcl 1gk6 1gzl 1ihq 1ij0 1ij1 1ij2 1ij3 1kql 1ld4 1llm 1nkn 1piq 1rb4 1rb5 1rb6 1swi 1tmz 1unt 1unu 1unv 1unw 1unx 1uny 1unz 1uo0 1uo1 1uo2 1uo3 1uo4 1uo5 1w5g 1w5h 1w5i 1w5j 1w5k 1w5l 1ysa 1zii 1zij 1zik 1zil 1zim 1zta 2b1f 2b22 2bni 2cce 2ccf 2ccn 2d3e 2dgc 2wg5 2wg6 2wpq 2wpr 2wps 2wpy 2wpz 2wq0 2wq1 2wq2 2wq3 2zta 3k7z S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2v71-d 4ke2-d 4cpc-1 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

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

2v71-d

4ke2-d

4cpc-1

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#70 - Oct 2005 Designer Proteins similarity (9) #122 - Feb 2010 Enhanceosome similarity (4)

Deposited unit

A: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

B: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

C: GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4

hetero molecules

86.8 kDa, 3 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)	189.320, 46.170, 103.760
Angle α, β, γ (deg.)	90.00, 98.03, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
1	2	A
2	2	B
3	2	C

NCS domain segments:

Component-ID: 1 / End auth comp-ID: LYS / End label comp-ID: LYS

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Refine code	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LYS	LYS	6	A	A	1157 - 1388	2 - 233
2	1	MET	MET	6	B	B	1156 - 1388	1 - 233
3	1	MET	MET	6	C	C	1156 - 1388	1 - 233
1	2	GLN	GLN	3	A	A	1389 - 1413	234 - 258
2	2	GLN	GLN	3	B	B	1389 - 1413	234 - 258
3	2	GLN	GLN	3	C	C	1389 - 1413	234 - 258

NCS ensembles :

ID
1
2

#1: Protein	GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN, GENERAL CONTROL PROTEIN GCN4 / AMINO ACID BIOSYNTHESIS REGULATORY PROTEIN / AUTOTRANSPORTER ADHESIN FRAGMENT Mass: 28931.012 Da / Num. of mol.: 3 Fragment: GCN4 ADAPTOR RESIDUES 250-278, ADHESIN RESIDUES 1185-1386, GCN4 ADAPTOR RESIDUES 250-278 Mutation: YES Source method: isolated from a genetically manipulated source Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: Q8ZL64
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	Details: 12% (W/V) PEG 8000, 100 MM MAGNESIUM ACETATE, 100 MM TRIS PH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
Detector	Type: MARRESEARCH / Detector: CCD / Date: Sep 29, 2008
Radiation	Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→37.3 Å / Num. obs: 59695 / % possible obs: 98.3 % / Redundancy: 3.91 % / R_merge(I) obs: 0.07 / Net I/σ(I): 12.4
Reflection shell	Resolution: 2→2.12 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.61 / Mean I/σ(I) obs: 2.32 / % possible all: 96.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GCM

1gcm

Resolution: 2→37.31 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.919 / SU B: 10.465 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.25292	2984	5 %	RANDOM
R_work	0.19983	-	-	-
obs	0.20238	56706	98.34 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 31.737 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.69 Å²	0 Å²	2.04 Å²
2-	-	0.51 Å²	0 Å²
3-	-	-	2.75 Å²

Refinement step

Cycle: LAST / Resolution: 2→37.31 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5652	0	1	573	6226

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	5701
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3577
X-RAY DIFFRACTION	r_angle_refined_deg	1.099	1.939	7728
X-RAY DIFFRACTION	r_angle_other_deg	0.854	3	8879
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.804	5	778
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.299	26.96	250
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.336	15	1001
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.891	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.065	0.2	955
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	6534
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	974
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.224	3	3815
X-RAY DIFFRACTION	r_mcbond_other	0.315	3	1602
X-RAY DIFFRACTION	r_mcangle_it	2.079	6	6128
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.847	9	1886
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.464	12	1595
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
2	1	A	150	tight positional	0.02	0.05
2	2	B	150	tight positional	0.02	0.05
2	3	C	150	tight positional	0.02	0.05
1	1	A	2647	loose positional	1.64	5
1	2	B	2647	loose positional	1.69	5
1	3	C	2647	loose positional	1.71	5
2	1	A	105	loose positional	0.03	5
2	2	B	105	loose positional	0.03	5
2	3	C	105	loose positional	0.03	5
2	1	A	150	tight thermal	0.08	0.5
2	2	B	150	tight thermal	0.05	0.5
2	3	C	150	tight thermal	0.05	0.5
1	1	A	2647	loose thermal	2	10
1	2	B	2647	loose thermal	1.91	10
1	3	C	2647	loose thermal	2.03	10
2	1	A	105	loose thermal	0.07	10
2	2	B	105	loose thermal	0.05	10
2	3	C	105	loose thermal	0.05	10

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.304	210	-
R_work	0.268	4024	-
obs	-	-	95.58 %

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	18.6552	1.6512	-2.4962	0.8618	-0.2245	1.2103	0.085	0.0795	0.1205	0.0303	0.0255	0.0915	-0.0245	0.0901	-0.1105	0.2239	0.0322	0.0033	0.0319	0.0131	0.1751	119.646	21.6715	15.2161
2	4.0615	0.1096	-0.1233	3.0407	-0.6316	1.9124	-0.0036	0.064	0.3429	-0.0787	-0.0503	-0.2849	-0.0711	0.2225	0.054	0.1346	0.027	-0.0288	0.0755	-0.014	0.0732	48.0696	26.6862	21.5468
3	3.5516	0.3742	-0.9621	1.965	-0.2589	1.4067	-0.0157	-0.1569	0.0039	-0.1662	0.0232	-0.0106	0.0505	0.0741	-0.0075	0.1746	0.0289	0.0167	0.1002	0.0149	0.2338	5.649	23.8243	26.8178
4	32.4535	-0.758	-12.9831	0.4488	-0.0611	5.5186	-0.1967	0.4444	-0.6077	-0.0596	-0.0257	0.0586	0.1203	-0.2634	0.2225	0.3568	-0.0273	-0.0041	0.6225	-0.037	0.2296	-49.3613	22.465	51.5038
5	15.2958	-1.4666	-2.5202	1.1476	-0.1191	1.3769	0.0084	0.5542	-0.0363	-0.0817	0.0266	0.1507	0.0334	-0.1232	-0.0349	0.2285	0.0064	-0.0077	0.1075	0.0093	0.1279	119.468	21.0976	8.3425
6	4.5466	-0.8291	0.5024	2.275	-0.6163	2.0014	-0.0539	-0.3105	0.2152	0.1525	-0.0096	-0.2216	-0.0362	0.331	0.0634	0.1307	0.0053	-0.0119	0.1289	-0.0251	0.0319	49.3843	23.3046	28.7988
7	5.9932	0.2292	-1.2636	2.2945	-1.2122	2.1886	0.0214	-0.7225	0.2577	0.2496	-0.049	-0.0755	-0.1691	0.2174	0.0276	0.1916	0.0151	0.0146	0.151	-0.0384	0.1756	6.165	26.1509	31.9115
8	40.4143	0.2793	-16.417	0.0178	-0.0544	8.1183	-0.3435	2.683	-0.9281	-0.0126	-0.0938	-0.0267	0.0936	-1.9141	0.4374	0.3301	0.0037	0.0468	0.933	-0.2362	0.5036	-49.2116	21.149	42.2675
9	18.2752	-0.0921	-7.4426	0.6388	0.0041	3.874	0.1785	0.3527	0.4701	-0.0785	0.0403	0.1063	-0.1178	-0.074	-0.2187	0.2028	0.0141	-0.0018	0.0355	0.0274	0.1964	119.2631	27.526	10.7373
10	3.7626	-0.8752	-0.9188	2.6372	-0.0515	2.4907	-0.0323	-0.1234	-0.0811	-0.0787	0.0292	-0.1454	0.15	0.2702	0.0031	0.1324	0.0122	-0.0245	0.0818	-0.0157	0.0249	48.4189	18.7907	22.3138
11	3.4027	-0.0344	-1.1048	1.7798	0.6857	1.333	-0.026	-0.4882	-0.1317	0.2134	0.0359	0.0008	0.1326	0.0967	-0.0099	0.2062	0.0191	0.0182	0.1523	0.0268	0.2238	6.2073	20.6767	31.3152
12	48.9553	0.6646	-18.9637	0.4769	-0.0344	7.7608	0.6339	0.2183	1.7244	0.1284	0.1126	0.1915	-0.182	-0.4853	-0.7465	0.3366	0.1051	0.0523	0.71	0.2437	0.3817	-49.987	30.2539	46.1208

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1157 - 1219
2	X-RAY DIFFRACTION	2	A	1220 - 1306
3	X-RAY DIFFRACTION	3	A	1307 - 1357
4	X-RAY DIFFRACTION	4	A	1358 - 1413
5	X-RAY DIFFRACTION	5	C	1157 - 1219
6	X-RAY DIFFRACTION	6	C	1220 - 1306
7	X-RAY DIFFRACTION	7	C	1307 - 1357
8	X-RAY DIFFRACTION	8	C	1358 - 1413
9	X-RAY DIFFRACTION	9	B	1156 - 1219
10	X-RAY DIFFRACTION	10	B	1220 - 1306
11	X-RAY DIFFRACTION	11	B	1307 - 1357
12	X-RAY DIFFRACTION	12	B	1358 - 1413

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