PDB-4oan: Crystal structure of a TRAP periplasmic solute binding protein fr...

ID or keywords:

Entry

Database: PDB / ID: 4oan

Title

Crystal structure of a TRAP periplasmic solute binding protein from rhodopseudomonas palustris HaA2 (RPB_2686), TARGET EFI-510221, with density modeled as (S)-2-hydroxy-2-methyl-3-oxobutanoate ((S)-2-Acetolactate)

Components

TRAP dicarboxylate transporter DctP subunit

Keywords

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

Function / homology

Function and homology information

transmembrane transport / outer membrane-bounded periplasmic space
Similarity search - Function

Biological species

Rhodopseudomonas palustris (phototrophic)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.35 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	Jan 5, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 22, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 25, 2015	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4oan.cif.gz	367.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4oan.ent.gz	319.6 KB	Display	PDB format
PDBx/mmJSON format	4oan.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4oan_validation.pdf.gz	461 KB	Display	wwPDB validaton report
Full document	4oan_full_validation.pdf.gz	463 KB	Display
Data in XML	4oan_validation.xml.gz	32.6 KB	Display
Data in CIF	4oan_validation.cif.gz	52 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oa/4oan ftp://data.pdbj.org/pub/pdb/validation_reports/oa/4oan	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 4napC 4nf0C 4ng7C 4nguC 4nhbC 4nn3C 4nq8C 4nx1C 4o7mC 4o8mC 4o94C 4oa4C 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	7bbr-d 4ovs-2 5jzn-1 7awc-d 5swh-2 2a4l-d 4xld-d 6e6e-2 6hzu-2 4yzh-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: EFI-510221

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (3) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: TRAP dicarboxylate transporter DctP subunit

B: TRAP dicarboxylate transporter DctP subunit

hetero molecules

75.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TRAP dicarboxylate transporter DctP subunit

hetero molecules

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

2

B: TRAP dicarboxylate transporter DctP subunit

hetero molecules

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

Unit cell

Length a, b, c (Å)	55.064, 59.609, 61.005
Angle α, β, γ (deg.)	62.620, 71.240, 67.180
Int Tables number	1
Space group name H-M	P1

#1: Protein	TRAP dicarboxylate transporter DctP subunit Mass: 37364.867 Da / Num. of mol.: 2 / Fragment: UNP residues 30-339 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: HaA2 / Gene: RPB_2686 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2IWM2
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-X2X / (2S)-2-hydroxy-2-methyl-3-oxobutanoic acid Mass: 132.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₈O₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 914 / 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: 2.16 Å³/Da / Density % sol: 43.03 %
Crystal grow	Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 6.9 Details: Protein (29.4 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.2 M Sodium Thiocyanate pH 6.9, 20 %(w/v) PEG 3350); Cryoprotection (Reservoir with 20% Glycerol), sitting drop vapor diffusion, 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: Nov 26, 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: 1.35→53.334 Å / Num. all: 129995 / Num. obs: 129995 / % possible obs: 94.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / B_iso Wilson estimate: 9.19 Å² / R_merge(I) obs: 0.069 / R_sym value: 0.069 / Net I/σ(I): 11.8

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
1.35-1.42	3.9	0.532	1.4	73193	18628	0.532	92.6
1.42-1.51	3.9	0.374	1.9	69562	17655	0.374	93.1
1.51-1.61	3.9	0.25	2.8	66209	16787	0.25	94
1.61-1.74	3.9	0.171	4.1	61985	15721	0.171	94.5
1.74-1.91	3.9	0.113	6.2	57243	14524	0.113	95.2
1.91-2.13	3.9	0.069	10.3	51896	13243	0.069	95.9
2.13-2.46	3.9	0.047	15.2	45476	11728	0.047	96.5
2.46-3.02	3.8	0.036	19.1	38243	9975	0.036	96.9
3.02-4.27	3.8	0.027	24.2	29063	7697	0.027	96.7
4.27-50.729	3.6	0.026	25	14623	4037	0.026	93.4

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.14	data extraction
MOSFLM		data reduction
PHENIX	AUTOSOLVE	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.35→31.401 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.9171 / SU ML: 0.11 / σ(F): 0 / σ(I): 0 / Phase error: 15.52 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1625	6523	5.02 %	RANDOM
R_work	0.1429	-	-	-
all	0.1439	129985	-	-
obs	0.1439	129985	94.62 %	-

Solvent computation

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

Displacement parameters

B_iso max: 103.15 Å² / B_iso mean: 13.9507 Å² / B_iso min: 4.38 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→31.401 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4846	0	25	914	5785

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5028
X-RAY DIFFRACTION	f_angle_d	1.281	6827
X-RAY DIFFRACTION	f_chiral_restr	0.077	740
X-RAY DIFFRACTION	f_plane_restr	0.008	889
X-RAY DIFFRACTION	f_dihedral_angle_d	12.731	1824

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.35-1.3653	0.2739	228	0.2415	4010	4238	93
1.3653-1.3814	0.2374	227	0.2291	4041	4268	92
1.3814-1.3983	0.2623	191	0.2181	3977	4168	93
1.3983-1.416	0.2278	220	0.2084	4061	4281	92
1.416-1.4346	0.2378	177	0.1994	4037	4214	93
1.4346-1.4542	0.2342	221	0.1919	4115	4336	93
1.4542-1.475	0.2092	199	0.1889	4043	4242	93
1.475-1.497	0.1794	197	0.1766	4061	4258	94
1.497-1.5204	0.2054	228	0.1669	4059	4287	93
1.5204-1.5453	0.1913	220	0.1599	4028	4248	94
1.5453-1.572	0.1678	225	0.156	4123	4348	94
1.572-1.6006	0.1669	225	0.1522	4072	4297	94
1.6006-1.6314	0.1706	225	0.1467	4068	4293	94
1.6314-1.6647	0.1727	234	0.1403	4103	4337	95
1.6647-1.7009	0.1577	195	0.1353	4149	4344	94
1.7009-1.7404	0.1625	243	0.135	4118	4361	95
1.7404-1.7839	0.1548	222	0.1267	4124	4346	95
1.7839-1.8322	0.1395	240	0.1249	4092	4332	95
1.8322-1.8861	0.1562	214	0.1264	4156	4370	95
1.8861-1.9469	0.1541	221	0.1299	4143	4364	96
1.9469-2.0165	0.1554	243	0.125	4126	4369	96
2.0165-2.0972	0.1428	210	0.1262	4211	4421	96
2.0972-2.1927	0.1458	213	0.1246	4236	4449	96
2.1927-2.3082	0.1502	205	0.129	4176	4381	96
2.3082-2.4528	0.159	208	0.13	4222	4430	97
2.4528-2.6421	0.1467	217	0.1314	4208	4425	97
2.6421-2.9078	0.1548	240	0.136	4185	4425	97
2.9078-3.3282	0.1562	225	0.1353	4236	4461	97
3.3282-4.1916	0.141	220	0.1298	4187	4407	97
4.1916-31.4092	0.148	190	0.149	4095	4285	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	0.034	0.0349	-0.0371	0.3145	0.117	0.1264	-0.0001	0.0009	-0.1572	0.0525	0.0329	-0.1444	0.1775	0.0803	-0.0149	0.099	0.0264	-0.0119	0.09	0.0013	0.1322	101.3862	52.2638	59.7951
2	1.0157	-0.1151	0.0843	0.5247	-0.1749	0.8946	-0.0286	0.0625	-0.0454	-0.0148	0.0485	-0.2151	-0.0424	0.0296	-0.0196	0.0955	0.0134	0.0195	0.1033	-0.0205	0.1619	104.5786	53.6691	54.1091
3	0.648	-0.1165	0.1603	0.5363	0.0359	0.5131	-0.0106	0.0005	0.022	-0.0023	-0.0108	-0.0858	-0.0309	0.0793	0.0224	0.055	-0.0026	0.0023	0.0688	0.0031	0.062	95.7985	71.0124	58.3877
4	0.3288	0.0316	0.1479	0.6911	0.0118	0.8033	-0.0068	-0.0445	0.0697	-0.0102	0.0039	0.0815	-0.1058	-0.0577	-0.0081	0.0624	0.0136	0.004	0.0777	-0.0085	0.0738	75.7477	75.4953	57.5501
5	0.5703	-0.1222	-0.004	0.3984	-0.1013	0.2849	-0.0231	-0.0345	0.0088	-0.0271	0.0193	0.0002	0.0072	-0.0128	-0.0061	0.0515	-0.0005	-0.0011	0.0507	-0.0026	0.0443	86.0427	64.8858	55.549
6	2.1976	-0.21	0.8324	0.4838	-0.1546	0.5727	0.0515	0.2892	0.0469	-0.1121	-0.0477	-0.0597	0.0612	0.1586	-0.0019	0.0858	0.0006	0.014	0.1038	-0.0079	0.0659	98.5796	63.133	46.9445
7	0.6249	0.2495	0.1641	1.1726	0.827	1.3677	-0.0337	-0.0464	0.0372	-0.0875	0.049	0.0008	-0.1334	-0.0651	-0.0238	0.0964	0.0058	-0.0166	0.0582	0.001	0.0685	76.9471	79.7576	47.114
8	0.9852	0.1142	-0.0084	0.8671	-0.0308	1.9968	0.0358	0.0035	0.0955	-0.0805	-0.0797	-0.1625	-0.1996	0.1899	0.0332	0.1319	-0.009	0.0057	0.0615	0.0013	0.1059	93.484	87.8939	55.7439
9	0.4976	0.0927	0.1446	0.4642	0.0599	0.5124	-0.0292	-0.05	0.0849	0.042	-0.0019	0.0062	-0.1588	-0.048	0.0217	0.1025	0.0066	0.0052	0.0606	-0.0057	0.0642	59.9147	53.9537	31.6029
10	0.4653	0.0194	-0.0525	0.4637	-0.17	0.7022	0.0011	0.0046	-0.0605	-0.0433	0.0186	-0.0138	0.0593	-0.0045	-0.0184	0.0707	-0.0042	0.0085	0.0561	-0.0034	0.0693	55.9094	34.0138	23.0859
11	0.5852	-0.0525	0.0177	1.6306	0.1351	0.1449	-0.0536	-0.027	0.121	-0.0724	-0.0007	-0.1841	-0.1855	0.0411	0.0243	0.145	-0.0257	-0.0096	0.0413	-0.0112	0.0786	64.5761	60.1181	31.4141
12	0.8934	0.9656	0.3091	2.5937	0.3641	0.5235	0.0242	-0.1046	0.0768	0.1605	-0.0497	0.1593	-0.033	-0.0736	0.0167	0.0774	0.0099	0.0205	0.0848	-0.0124	0.0621	52.5601	51.8067	39.1276
13	1.7125	-0.0566	-0.3931	0.6084	0.0919	0.6697	-0.0271	-0.1484	-0.1042	-0.0945	-0.0016	-0.0613	0.0846	0.0502	0.0243	0.0825	-0.0036	0.0044	0.0628	0.0213	0.1077	59.366	26.2087	32.5474
14	1.4915	0.3835	-0.7673	0.8687	-0.346	1.553	-0.07	-0.1795	-0.0657	0.1338	-0.0127	-0.063	-0.0486	0.2164	0.0599	0.0754	0.0024	-0.0129	0.1215	0.0184	0.1069	75.3188	37.6554	37.9092

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 46 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 47 through 72 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 73 through 161 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 162 through 200 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201 through 258 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 259 through 293 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 294 through 314 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 315 through 339 )	A
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 30 through 161 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 162 through 241 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 242 through 258 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 259 through 293 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 294 through 314 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 315 through 339 )	B

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