PDB-4nap: Crystal structure of a trap periplasmic solute binding protein fr...

ID or keywords:

Entry

Database: PDB / ID: 4nap

Title

Crystal structure of a trap periplasmic solute binding protein from Desulfovibrio alaskensis G20 (DDE_0634), target EFI-510102, with bound d-tryptophan

Components

Extracellular solute-binding protein, family 7

Keywords

TRANSPORT PROTEIN / TRAP PERIPLASMIC SOLUTE BINDING FAMILY / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

transmembrane transport / periplasmic space
Similarity search - Function

Biological species

Desulfovibrio alaskensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.3 Å

Authors

Vetting, M.W. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Evans, B. ...

Citation

Journal: Biochemistry / Year: 2015
Title: Experimental strategies for functional annotation and metabolism discovery: targeted screening of solute binding proteins and unbiased panning of metabolomes.
Authors: Vetting, M.W. / Al-Obaidi, N. / Zhao, S. / San Francisco, B. / Kim, J. / Wichelecki, D.J. / Bouvier, J.T. / Solbiati, J.O. / Vu, H. / Zhang, X. / Rodionov, D.A. / Love, J.D. / Hillerich, B.S. ...

History

Deposition	Oct 22, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 13, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 25, 2015	Group: Database references
Revision 1.2	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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	4nap.cif.gz	695.5 KB	Display	PDBx/mmCIF format
PDB format	pdb4nap.ent.gz	597.2 KB	Display	PDB format
PDBx/mmJSON format	4nap.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nap_validation.pdf.gz	468.9 KB	Display	wwPDB validaton report
Full document	4nap_full_validation.pdf.gz	482.4 KB	Display
Data in XML	4nap_validation.xml.gz	55.3 KB	Display
Data in CIF	4nap_validation.cif.gz	72.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/na/4nap ftp://data.pdbj.org/pub/pdb/validation_reports/na/4nap	HTTPS FTP

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Related structure data

Related structure data	4ln5C 4mcoC 4mevC 4mhfC 4mijC 4mncC 4mniC 4mx6C 4n15C 4n17C 4n4uC 4n6dC 4n6kC 4n8gC 4n8yC 4n91C 4nf0C 4ng7C 4nguC 4nhbC 4nn3C 4nq8C 4nx1C 4o7mC 4o8mC 4o94C 4oa4C 4oanC 4ovpC 4ovqC 4ovrC 4ovsC 4ovtC 4p1eC 4p1lC 4p3lC 4p47C 4p56C 4p8bC 4p9kC 4pafC 4paiC 4pakC 4pbhC 4pbqC 4pc9C 4pcdC 4pddC 4pdhC 4pe3C 4petC 4pf6C 4pf8C 4pfbC 4pfiC 4pfrC 4pgnC 4pgpC 4uabC C: citing same article (ref.)
Similar structure data	4pgn-2 4pgp-3 4pgp-1 3ae0-1 4pbq-3 4pgp-4 3ezv-d 4p1l-2 5i7i-2 5lpv-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: EFI-510102

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Extracellular solute-binding protein, family 7

B: Extracellular solute-binding protein, family 7

C: Extracellular solute-binding protein, family 7

D: Extracellular solute-binding protein, family 7

hetero molecules

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

1

A: Extracellular solute-binding protein, family 7

hetero molecules

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

2

B: Extracellular solute-binding protein, family 7

hetero molecules

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

3

C: Extracellular solute-binding protein, family 7

hetero molecules

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

4

D: Extracellular solute-binding protein, family 7

hetero molecules

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

Unit cell

Length a, b, c (Å)	50.117, 144.571, 96.389
Angle α, β, γ (deg.)	90.000, 90.520, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Extracellular solute-binding protein, family 7 Mass: 35107.547 Da / Num. of mol.: 4 / Fragment: unp residues 30-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio alaskensis (bacteria) / Strain: G20 / Gene: Dde_0634 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q315G1
#2: Chemical	ChemComp-DTR / D-TRYPTOPHAN Type: D-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₂N₂O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 350 / Source method: isolated from a natural source / Formula: H₂O
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: 2.49 Å³/Da / Density % sol: 50.53 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Protein (50 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-TRYPTOPHAN); Reservoir (0.1 M Sodium Citrate, 20 %(v/v) iso-Propanol, 20 %(w/v) PEG 4000), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Oct 17, 2013 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 2.2→144.571 Å / Num. all: 69245 / Num. obs: 69245 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / B_iso Wilson estimate: 33.14 Å² / R_merge(I) obs: 0.082 / R_sym value: 0.082 / Net I/σ(I): 11.7

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
2.2-2.32	5.2	0.585	1.3	52660	10121	0.585	100
2.32-2.46	5.3	0.375	2.1	50392	9553	0.375	100
2.46-2.63	5.3	0.258	3	47747	9035	0.258	100
2.63-2.84	5.3	0.175	4.4	44338	8361	0.175	100
2.84-3.11	5.3	0.109	7	41077	7750	0.109	100
3.11-3.48	5.3	0.069	10.2	36774	6950	0.069	100
3.48-4.02	5.3	0.055	12.3	32482	6169	0.055	99.6
4.02-4.92	5.2	0.037	16.4	27199	5195	0.037	99.6
4.92-6.96	5.2	0.036	16.4	20953	4019	0.036	99.2
6.96-144.571	4.9	0.03	20	10261	2092	0.03	92.9

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
HKL-3000		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.3→31.426 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7983 / SU ML: 0.24 / σ(F): 0 / σ(I): 0 / Phase error: 26.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2154	3099	5.13 %	RANDOM
R_work	0.1627	-	-	-
obs	0.1655	60459	99.45 %	-
all	-	60459	-	-

Solvent computation

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

Displacement parameters

B_iso max: 147.35 Å² / B_iso mean: 44.2214 Å² / B_iso min: 9.69 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→31.426 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9487	0	60	350	9897

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	9780
X-RAY DIFFRACTION	f_angle_d	1.379	13309
X-RAY DIFFRACTION	f_chiral_restr	0.077	1486
X-RAY DIFFRACTION	f_plane_restr	0.008	1727
X-RAY DIFFRACTION	f_dihedral_angle_d	14.735	3552

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.3-2.3359	0.2801	135	0.2141	2576	2711	100
2.3359-2.3742	0.2623	144	0.187	2659	2803	100
2.3742-2.4152	0.2523	130	0.1852	2627	2757	100
2.4152-2.4591	0.2774	122	0.1806	2594	2716	100
2.4591-2.5063	0.215	134	0.1765	2657	2791	100
2.5063-2.5575	0.2637	141	0.1787	2583	2724	100
2.5575-2.6131	0.2421	147	0.173	2599	2746	100
2.6131-2.6738	0.2282	139	0.1776	2628	2767	100
2.6738-2.7406	0.227	130	0.1712	2639	2769	100
2.7406-2.8147	0.2336	141	0.1704	2598	2739	100
2.8147-2.8975	0.2504	135	0.1723	2620	2755	100
2.8975-2.9909	0.2211	148	0.1799	2609	2757	100
2.9909-3.0977	0.2349	155	0.1741	2609	2764	100
3.0977-3.2216	0.2395	147	0.1768	2598	2745	100
3.2216-3.3681	0.2652	124	0.1685	2647	2771	100
3.3681-3.5454	0.2552	153	0.1595	2623	2776	100
3.5454-3.7672	0.2183	147	0.191	2564	2711	99
3.7672-4.0575	0.1801	129	0.1446	2582	2711	99
4.0575-4.4648	0.1519	157	0.1305	2621	2778	100
4.4648-5.1085	0.1709	155	0.1204	2619	2774	99
5.1085-6.4271	0.1883	132	0.1572	2623	2755	99
6.4271-31.4286	0.2171	154	0.1629	2485	2639	94

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	0.8814	0.5604	0.0185	4.7897	-0.8544	1.2469	-0.1213	0.064	0.3023	0.0666	0.2374	0.1908	-0.2112	-0.0007	-0.1129	0.2275	-0.0022	0.0211	0.2816	0.0241	0.3016	19.1358	17.2406	54.0803
2	5.4638	-1.5765	0.3047	5.4189	-0.6501	1.4564	-0.0538	-0.1551	0.159	0.0553	0.2521	0.7114	0.0363	-0.2906	-0.1446	0.1771	-0.0037	0.0067	0.268	0.0499	0.2944	11.2978	8.5908	53.2904
3	3.5668	-0.1505	-0.7087	3.5606	-0.1195	4.3364	0.0057	-0.1686	0.2607	0.3172	0.1195	-0.7508	-0.2608	0.4796	-0.0947	0.2875	0.0146	-0.0539	0.3819	-0.0592	0.4728	34.3073	0.9378	62.7557
4	3.6636	-2.0973	1.2028	5.0918	-1.4894	3.662	-0.0787	0.054	0.364	-0.3232	0.3629	0.5587	-0.3755	-0.453	-0.2579	0.2065	-0.0275	-0.0196	0.315	0.1111	0.4216	12.2849	15.7717	50.7387
5	1.0362	-0.2668	0.9038	1.5556	-1.0214	2.4159	-0.0828	0.3648	0.02	-0.4623	0.0264	-0.7193	0.3537	0.4842	0.044	0.326	-0.0086	0.1232	0.4528	-0.0538	0.4811	32.1703	-2.2031	50.2485
6	6.0432	-1.6999	1.2975	4.9512	-0.4278	5.4387	-0.0134	-0.0421	-0.0907	0.1492	0.1568	0.8196	0.3095	-0.7002	-0.1796	0.1945	-0.0366	0.0271	0.2557	0.0289	0.3429	8.6966	-4.2847	60.1309
7	0.9491	-0.0821	0.1762	3.0036	0.9527	0.9075	0.0197	0.1521	0.0651	-0.2978	0.0764	-0.3621	-0.1873	0.2052	-0.0877	0.1717	-0.0159	0.0471	0.1713	-0.0193	0.1685	31.9109	32.4914	91.1066
8	2.4348	0.7714	-0.0573	2.4355	0.5772	3.6358	0.0295	0.0409	0.0728	-0.124	-0.1413	0.4676	-0.1848	-0.4557	0.0974	0.1372	0.0082	0.0163	0.2321	-0.0199	0.242	14.6668	18.2485	82.36
9	4.7174	3.5554	0.1349	7.5845	-0.2134	2.4335	0.0463	-0.0904	0.1683	0.2335	-0.0658	-0.1747	-0.1622	0.0795	0.0704	0.07	0.02	0.0458	0.2333	-0.025	0.0872	29.8311	25.1025	89.1846
10	5.8427	2.0386	0.1579	4.4008	0.5835	3.3411	0.0407	-0.2656	-0.2369	0.3015	-0.0138	-0.3001	0.0339	-0.0065	-0.0364	0.1406	0.0581	-0.0181	0.1744	-0.0403	0.0801	27.9538	29.9078	99.1621
11	7.7776	-3.5434	-3.8927	1.6294	1.7195	4.6828	-0.2885	-0.5019	-0.4431	0.2469	-0.0395	0.4951	0.9341	-0.1315	0.3297	0.1575	-0.0674	0.061	0.2371	0.0223	0.5557	12.9602	6.4039	88.8249
12	3.4467	0.7416	1.7783	3.207	0.5843	4.3017	0.0159	0.372	-0.4458	0.0537	0.3385	-0.4266	0.1343	0.5656	-0.2955	0.1745	0.057	0.0639	0.2282	-0.0522	0.3762	38.4923	11.701	84.5161
13	3.8399	0.4957	1.1211	2.4491	0.7242	2.395	-0.2824	0.2037	-0.1315	-0.0174	0.2415	0.3139	-0.0808	-0.0256	0.0614	0.3616	-0.0666	-0.0146	0.2844	0.0962	0.3539	28.0856	31.9862	42.1964
14	2.0159	1.5598	1.0838	5.6534	0.0897	1.7471	-0.1103	0.2737	-0.297	-0.407	0.1568	-0.6407	0.0765	0.3149	-0.0444	0.3122	-0.016	0.0181	0.3438	0.0387	0.3106	41.5215	41.3241	39.4444
15	3.5226	-0.1438	0.399	0.5751	0.8991	3.5186	0.2399	-0.8862	-0.5806	1.0983	-0.3275	-0.7928	0.3024	0.3276	0.0485	0.8033	-0.067	-0.2423	0.6373	0.1276	0.5425	48.4137	42.8416	60.7133
16	4.5465	0.6184	0.1126	4.2781	-0.0469	3.2379	-0.1395	-0.0277	-0.07	-0.0113	0.07	0.214	0.4567	-0.1168	0.0897	0.3049	-0.0266	-0.0204	0.2188	0.1052	0.2217	32.3532	41.6305	42.5554
17	1.5652	-0.8364	-0.2358	1.7321	-1.5441	2.3648	0.0144	-0.5801	0.511	1.67	0.0736	-0.5848	-0.5316	-0.0198	0.0263	1.195	-0.1956	-0.1287	0.6921	-0.0545	0.3214	45.3176	53.6964	62.7767
18	6.4632	-1.8243	0.0903	3.4134	0.2996	2.5008	0.0272	0.0124	0.0932	-0.0999	-0.1492	-0.7037	-0.1636	0.65	0.0877	0.2985	-0.0881	0.0265	0.424	0.12	0.4609	46.924	56.696	37.4165
19	4.306	1.3575	2.4683	2.1294	1.173	3.2187	0.2312	0.0085	-0.2691	0.1741	-0.1117	-0.0568	0.2923	0.1314	-0.1339	0.173	0.0081	0.0248	0.0996	0.034	0.1853	28.0128	-23.2488	90.5306
20	1.6487	0.7493	0.7906	4.2703	0.2194	1.4275	-0.0192	0.1884	-0.1339	-0.1389	0.0196	-0.4214	0.061	0.3012	-0.0136	0.1842	0.0346	0.0306	0.2177	0.0148	0.1828	41.8285	-13.6914	87.1973
21	2.6544	-0.2002	1.465	1.7982	-0.4955	3.0273	0.0959	-0.2596	0.1346	0.5415	-0.0948	-0.2865	0.1393	0.441	0.0095	0.4237	-0.0059	-0.0919	0.3584	-0.0011	0.2722	46.8746	-12.5349	107.6618
22	3.6338	0.9306	2.6333	4.2187	1.4396	4.6404	0.0022	0.2612	0.1498	-0.2089	0.016	0.0793	0.2077	0.0934	-0.0184	0.1947	0.0317	0.0451	0.1171	0.0763	0.1277	33.3269	-15.4998	84.1803
23	1.1379	0.4518	1.5021	1.3033	0.1714	2.2717	0.1143	-0.6813	0.1515	1.2049	-0.0033	-0.0401	-0.6943	-0.3442	-0.0712	0.7357	-0.0242	-0.0406	0.3628	-0.0624	0.2075	35.1767	-6.8024	109.3562
24	5.0245	-0.8046	0.9363	2.5981	-1.8159	2.6449	-0.1437	0.1101	0.0649	0.4965	-0.2473	-0.2484	-0.2291	0.4205	0.4153	0.2707	-0.0434	-0.0088	0.2587	0.0676	0.4984	48.0972	2.1219	89.3527

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	(chain A and resid 32:120)	A	32 - 120
2	X-RAY DIFFRACTION	2	(chain A and resid 121:152)	A	121 - 152
3	X-RAY DIFFRACTION	3	(chain A and resid 153:229)	A	153 - 229
4	X-RAY DIFFRACTION	4	(chain A and resid 230:264)	A	230 - 264
5	X-RAY DIFFRACTION	5	(chain A and resid 265:305)	A	265 - 305
6	X-RAY DIFFRACTION	6	(chain A and resid 306:339)	A	306 - 339
7	X-RAY DIFFRACTION	7	(chain B and resid 31:150)	B	31 - 150
8	X-RAY DIFFRACTION	8	(chain B and resid 151:229)	B	151 - 229
9	X-RAY DIFFRACTION	9	(chain B and resid 230:244)	B	230 - 244
10	X-RAY DIFFRACTION	10	(chain B and resid 245:287)	B	245 - 287
11	X-RAY DIFFRACTION	11	(chain B and resid 288:302)	B	288 - 302
12	X-RAY DIFFRACTION	12	(chain B and resid 303:339)	B	303 - 339
13	X-RAY DIFFRACTION	13	(chain C and resid 32:71)	C	32 - 71
14	X-RAY DIFFRACTION	14	(chain C and resid 72:150)	C	72 - 150
15	X-RAY DIFFRACTION	15	(chain C and resid 151:229)	C	151 - 229
16	X-RAY DIFFRACTION	16	(chain C and resid 230:282)	C	230 - 282
17	X-RAY DIFFRACTION	17	(chain C and resid 283:310)	C	283 - 310
18	X-RAY DIFFRACTION	18	(chain C and resid 311:340)	C	311 - 340
19	X-RAY DIFFRACTION	19	(chain D and resid 32:73)	D	32 - 73
20	X-RAY DIFFRACTION	20	(chain D and resid 74:144)	D	74 - 144
21	X-RAY DIFFRACTION	21	(chain D and resid 145:229)	D	145 - 229
22	X-RAY DIFFRACTION	22	(chain D and resid 230:264)	D	230 - 264
23	X-RAY DIFFRACTION	23	(chain D and resid 265:302)	D	265 - 302
24	X-RAY DIFFRACTION	24	(chain D and resid 303:340)	D	303 - 340

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