PDB-3ny7: STAS domain of YchM bound to ACP

ID or keywords:

Entry

Database: PDB / ID: 3ny7

Title

STAS domain of YchM bound to ACP

Components

Acyl carrier protein
Sulfate transporter

Keywords

MEMBRANE PROTEIN / Fatty acid Biosynthesis(FAB) / Bicarbonate transport / anion transport / STAS domain / Acyl Carrier protein / SLC26 / YchM / 4'-Phosphopantetheine / Ser 36 of ACp

Function / homology

Function and homology information

fumarate transmembrane transporter activity / fumarate transport / succinate transmembrane transport / succinate transmembrane transporter activity / secondary active sulfate transmembrane transporter activity / aspartate transmembrane transport / L-aspartate transmembrane transport / L-aspartate transmembrane transporter activity / lipid biosynthetic process / lipid A biosynthetic process ...
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.922 Å

Authors

Moraes, T.F. / Reithmeier, R. / Strynadka, N.C.S.

Citation

Journal: Structure / Year: 2010
Title: Structure of a SLC26 Anion Transporter STAS Domain in Complex with Acyl Carrier Protein: Implications for E. coli YchM in Fatty Acid Metabolism.
Authors: Babu, M. / Greenblatt, J.F. / Emili, A. / Strynadka, N.C. / Reithmeier, R.A. / Moraes, T.F.

History

Deposition	Jul 14, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 1, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3ny7.cif.gz	96.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3ny7.ent.gz	75.2 KB	Display	PDB format
PDBx/mmJSON format	3ny7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ny7_validation.pdf.gz	1018 KB	Display	wwPDB validaton report
Full document	3ny7_full_validation.pdf.gz	1019.2 KB	Display
Data in XML	3ny7_validation.xml.gz	12.9 KB	Display
Data in CIF	3ny7_validation.cif.gz	18.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ny/3ny7 ftp://data.pdbj.org/pub/pdb/validation_reports/ny/3ny7	HTTPS FTP

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Related structure data

Similar structure data	3kot-d 3kos-d 4mo7-d 4fn2-1 4giv-1 6iom-1 2y7p-d 3d9t-d 4d8d-2 1s9h-3 Search similar-shape structures by Omokage search (details) 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	#90 - Jun 2007 Fatty Acid Synthase similarity (8) #183 - Mar 2015 Phototropin similarity (4)

Deposited unit

A: Sulfate transporter

B: Acyl carrier protein

hetero molecules

22.2 kDa, 2 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)	33.631, 55.867, 113.411
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Sulfate transporter / YchM protein Mass: 13042.310 Da / Num. of mol.: 1 / Fragment: UNP residues 436-550 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ychM / Production host: Escherichia coli (E. coli) / References: UniProt: C9QXZ0, UniProt: P0AFR2*PLUS
#2: Protein	Acyl carrier protein / ACP Mass: 8645.460 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: C5W3Z7, UniProt: P0A6A8*PLUS
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SXM / 3-{[2-({N-[(2S)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl]sulfanyl}-3-oxopropanoic acid / THIOMALONIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER Mass: 444.394 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₄H₂₅N₂O₁₀PS
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 2.46 Å³/Da / Density % sol: 49.92 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.1 Details: 20% PEG 8000, 10 mM Na Citrate , pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 105 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 28, 2009
Radiation	Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.92→50 Å / Num. all: 17084 / Num. obs: 16742 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.2 %
Reflection shell	Resolution: 1.92→1.99 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.338 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1371 / R_sym value: 0.347 / % possible all: 81.8

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Processing

Software

Name	Version	Classification
MAR345dtb		data collection
SHELX		model building
SHARP		phasing
PHENIX	(phenix.refine: 1.6.2_432)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
SHELX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.922→39.797 Å / SU ML: 0.22 / σ(F): 1.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.219	849	5.09 %	RANDOM
R_work	0.1623	-	-	-
all	0.165	16742	-	-
obs	0.165	16690	98.4 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40.971 Å² / k_sol: 0.357 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.7801 Å²	-0 Å²	0 Å²
2-	-	-6.0018 Å²	-0 Å²
3-	-	-	2.2217 Å²

Refinement step

Cycle: LAST / Resolution: 1.922→39.797 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1513	0	33	231	1777

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1604
X-RAY DIFFRACTION	f_angle_d	1.015	2171
X-RAY DIFFRACTION	f_dihedral_angle_d	17.24	643
X-RAY DIFFRACTION	f_chiral_restr	0.063	246
X-RAY DIFFRACTION	f_plane_restr	0.011	285

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 (%)
1.922-2.0423	0.3033	139	0.2081	2376	X-RAY DIFFRACTION	91
2.0423-2.2	0.2334	144	0.1654	2604	X-RAY DIFFRACTION	99
2.2-2.4214	0.2156	149	0.1534	2653	X-RAY DIFFRACTION	100
2.4214-2.7717	0.2123	150	0.1575	2641	X-RAY DIFFRACTION	100
2.7717-3.4917	0.2175	149	0.1607	2700	X-RAY DIFFRACTION	100
3.4917-39.8056	0.1982	118	0.1589	2867	X-RAY DIFFRACTION	100

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	0.1724	-0.092	-0.0684	0.1076	0.0053	0.0625	0.5921	-0.2517	0.1683	-0.0918	-0.6054	-0.9454	-0.2347	0.2552	-0.0004	0.1858	-0.051	0.0591	0.2513	-0.002	0.3254	43.5173	29.8009	40.628
2	0.1198	-0.0247	0.0294	0.0012	-0.0019	0.0083	0.0778	0.3593	-0.0698	0.4841	0.1306	-0.8249	0.3736	0.4772	0.0004	0.304	0.0711	-0.0597	0.1977	-0.0003	0.3357	39.0792	9.11	39.8802
3	-0.0086	0.001	-0.0022	0.0332	-0.027	0.0192	-0.0147	0.1285	-0.1098	0.2087	-0.1647	-0.0627	0.0737	0.0229	0.0001	0.195	0.011	0.0105	0.1351	0.0133	0.1379	37.2934	16.2845	39.7612
4	0.0154	-0.0489	-0.0184	0.0429	0.0275	0.0186	0.1453	0.0254	0.0249	0.0996	-0.2465	-0.0953	-0.3857	0.0471	-0.0001	0.1568	0.0026	0.0102	0.1499	0.0278	0.1489	35.6813	32.5351	39.7981
5	0.0947	0.0671	0.0503	0.048	0.0132	0.0894	0.0983	-0.0162	-0.0357	-0.1646	-0.1902	-0.4182	-0.1161	-0.0231	-0.0001	0.2005	-0.0085	0.0266	0.1733	0.0267	0.1835	37.7039	28.1286	32.5521
6	0.0464	-0.0117	-0.0507	0.1037	0.14	0.1594	0.1377	0.5066	-0.1261	-0.1471	-0.0751	-0.1385	0.1252	-0.0258	-0	0.1842	0.0024	0.0397	0.185	-0.0173	0.1545	36.8794	15.2702	29.5089
7	0.053	-0.0307	0.0036	0.0652	-0.0398	0.0178	0.0855	0.0177	0.0981	0.1826	0.0229	-0.2968	0.3386	0.0526	-0.0002	0.1765	0.0045	0.0136	0.1217	0.0191	0.1247	32.5543	20.5823	41.8685
8	0.1677	0.042	-0.0646	0.1069	-0.0532	0.0318	0.1105	-0.0318	0.1488	-0.1483	0.1343	-0.0454	-0.0187	-0.3148	-0.0001	0.169	0.026	0.0084	0.1476	0.0172	0.1295	29.5897	32.3379	38.532
9	0.0375	-0.0414	0.0243	0.03	-0.0206	0.0115	0.1829	0.152	0.1226	-0.7212	-0.136	-0.1915	-0.1451	0.0094	-0.0004	0.2715	0.0409	0.0057	0.1844	0.0315	0.1359	28.3898	26.7308	28.1684
10	0.4289	-0.4416	0.0663	0.381	-0.0124	0.1072	0.114	0.023	-0.0015	-0.1494	0.0977	-0.0527	-0.0814	-0.2381	-0.0002	0.1508	-0.007	0.0124	0.1192	-0.0018	0.108	28.8413	18.2727	33.2769
11	0.1429	0.0281	-0.0959	0.0369	-0.0463	0.0698	-0.0952	-0.0387	0.1214	0.3071	0.0214	0.1799	0.2993	0.0701	-0	0.1504	0.0106	0.0214	0.1071	0.0071	0.1391	23.8037	30.82	45.456
12	0.0143	0.0633	0.0142	0.3069	-0.0393	0.0972	-0.2203	0.1338	-0.0658	0.2466	-0.2002	0.9981	-0.2337	-0.2911	-0.002	0.2064	0.0644	-0.046	0.2233	0.012	0.2077	18.3441	27.3267	36.8357
13	-0.0012	-0.0304	-0.0035	0.0687	0.0204	0.0028	0.1533	0.149	-0.266	-0.0391	0.0616	0.088	0.3231	0.1525	-0.0001	0.1593	0.0364	-0.0184	0.1375	-0.0168	0.1165	23.5125	17.8727	36.2956
14	0.0363	-0.0519	0.0267	0.1609	-0.106	0.058	0.0373	-0.0335	-0.0464	-0.1838	-0.0887	0.2344	0.0913	-0.1227	-0.0003	0.1688	0.0026	0.0175	0.1058	0.0247	0.1121	28.4379	10.1644	44.0582
15	0.0557	-0.0714	-0.0118	0.064	0.0075	0.0355	-0.2526	-0.0448	0.0741	0.4638	0.2237	0.232	0.1338	0.0279	-0.0001	0.1853	0.0277	0.0138	0.1613	0.0319	0.2151	3.3138	35.0274	61.4575
16	-0.0121	0.023	-0.0125	0.0759	-0.0255	0.0739	-0.0995	-0.0415	0.0772	-0.0435	0.1777	0.3162	-0.0989	0.0433	-0.0001	0.1601	0.0037	-0.0192	0.1257	0.0152	0.1475	6.2929	27.666	54.5775
17	0.0337	0.0181	-0.0126	0.0215	0.0078	0.0466	0.227	0.022	0.2523	0.114	0.1906	0.6609	0.4393	-0.6926	-0.0003	0.2056	-0.0454	-0.0154	0.2804	0.071	0.2764	3.4254	20.5065	58.8972
18	0.0363	0.0078	-0.0417	-0.0015	-0.0064	0.0236	-0.0708	-0.1466	-0.1802	0.1483	-0.0645	-0.132	0.0199	0.1465	-0.0001	0.1596	-0.0102	-0.0125	0.1631	0.0195	0.164	12.4443	23.5364	62.2953
19	0.1067	0.0152	-0.1122	0.0647	0.0314	0.1271	0.0421	-0.0931	-0.095	0.0302	-0.1851	-0.0149	-0.0315	0.2401	-0	0.0909	-0.0211	0.0063	0.1665	0.0153	0.1427	16.1869	22.1192	53.2106
20	0.0456	-0.0222	0.0386	0.0686	0.0644	0.0909	-0.0521	0.1863	0.1511	-0.0301	0.0098	-0.2562	-0.1408	0.1095	0.0001	0.0846	-0.0235	0.0079	0.178	0.0165	0.1358	12.0552	34.3412	50.1288
21	0.1705	0.07	-0.1563	0.0965	-0.0217	0.1285	0.0162	0.0523	0.3853	0.0309	0.1037	-0.1317	-0.0986	0.0493	0.0001	0.1376	0.0068	-0.0049	0.1702	0.0027	0.2457	18.6233	39.2808	53.9816
22	-0.0069	0.0201	-0.0086	0.0637	0.0019	0.1295	0.1046	-0.2349	-0.1213	0.2157	-0.1649	-0.4949	-0.4073	0.2231	-0	0.1575	-0.0193	-0.0091	0.1117	0.0254	0.1974	16.9897	32.0033	61.1957
23	0.0433	0.0568	0.0055	0.0613	0.0066	0.0042	-0.0865	-0.0319	0.2475	0.1914	0.0678	0.3014	-0.1003	0.1789	-0.0007	0.1965	-0.0192	0.028	0.1957	-0.0226	0.2439	14.0656	42.5472	61.2514

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 433:440)
2	X-RAY DIFFRACTION	2	(chain A and resid 441:449)
3	X-RAY DIFFRACTION	3	(chain A and resid 450:454)
4	X-RAY DIFFRACTION	4	(chain A and resid 455:462)
5	X-RAY DIFFRACTION	5	(chain A and resid 463:471)
6	X-RAY DIFFRACTION	6	(chain A and resid 472:480)
7	X-RAY DIFFRACTION	7	(chain A and resid 481:486)
8	X-RAY DIFFRACTION	8	(chain A and resid 487:499)
9	X-RAY DIFFRACTION	9	(chain A and resid 500:504)
10	X-RAY DIFFRACTION	10	(chain A and resid 505:517)
11	X-RAY DIFFRACTION	11	(chain A and resid 518:525)
12	X-RAY DIFFRACTION	12	(chain A and resid 526:533)
13	X-RAY DIFFRACTION	13	(chain A and resid 534:541)
14	X-RAY DIFFRACTION	14	(chain A and resid 542:550)
15	X-RAY DIFFRACTION	15	(chain B and resid 2:8)
16	X-RAY DIFFRACTION	16	(chain B and resid 9:16)
17	X-RAY DIFFRACTION	17	(chain B and resid 17:22)
18	X-RAY DIFFRACTION	18	(chain B and resid 23:30)
19	X-RAY DIFFRACTION	19	(chain B and resid 31:41)
20	X-RAY DIFFRACTION	20	(chain B and resid 42:50)
21	X-RAY DIFFRACTION	21	(chain B and resid 51:60)
22	X-RAY DIFFRACTION	22	(chain B and resid 61:72)
23	X-RAY DIFFRACTION	23	(chain B and resid 73:78)

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