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

ID or keywords:

Entry

Database: PDB / ID: 4nhb

Title

Crystal structure of a TRAP periplasmic solute binding protein from Desulfovibrio desulfuricans (Ddes_1525), Target EFI-510107, with bound sn-glycerol-3-phosphate

Components

TRAP dicarboxylate transporter-DctP subunit

Keywords

TRANSPORT PROTEIN / TRAP periplasmic solute binding family / Enzyme Function Initiative / EFI / structural genomics

Function / homology

Function and homology information

transmembrane transport
Similarity search - Function

Biological species

Desulfovibrio desulfuricans subsp. desulfuricans (bacteria)

Method

X-RAY DIFFRACTION /

SAD / Resolution: 1.902 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	Nov 4, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 20, 2013	Provider: repository / Type: Initial release
Revision 1.1	Feb 25, 2015	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Feb 28, 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	4nhb.cif.gz	351.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4nhb.ent.gz	293.1 KB	Display	PDB format
PDBx/mmJSON format	4nhb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4nhb_validation.pdf.gz	457.9 KB	Display	wwPDB validaton report
Full document	4nhb_full_validation.pdf.gz	466.1 KB	Display
Data in XML	4nhb_validation.xml.gz	28.9 KB	Display
Data in CIF	4nhb_validation.cif.gz	42.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nh/4nhb ftp://data.pdbj.org/pub/pdb/validation_reports/nh/4nhb	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 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	2vpo-2 5lvm-d 3fxb-1 4oa4-2 4o7m-1 6hzv-3 4xeq-4 4i6q-d 3bhh-1 6ntp-d 4mni-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-510107

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TRAP dicarboxylate transporter-DctP subunit

B: TRAP dicarboxylate transporter-DctP subunit

hetero molecules

78.6 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
39.5 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
39.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	53.090, 83.407, 65.043
Angle α, β, γ (deg.)	90.000, 91.830, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	TRAP dicarboxylate transporter-DctP subunit / TRAP periplasmic solute binding protein Mass: 37647.238 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans (bacteria) Strain: ATCC 27774 / DSM 6949 / Gene: Ddes_1525 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B8J100
#2: Chemical	... ChemComp-IOD / IODIDE ION Mass: 126.904 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-G3P / SN-GLYCEROL-3-PHOSPHATE Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₉O₆P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 434 / 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: 1.91 Å³/Da / Density % sol: 35.66 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 33.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000, cryoprotection: 4:1 50% PEG3350, 500 mM NaI:reservoir (3 ...Details: 33.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000, cryoprotection: 4:1 50% PEG3350, 500 mM NaI:reservoir (3 minutes), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal

Density Matthews: 1.91 Å³/Da / Density % sol: 35.66 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 33.8 mg/mL protein in 10 mM HEPES, pH 7.5, 5 mM DTT, reservoir: 0.2 M magnesium chloride, 0.1 M Tris, pH 8.5, 30% w/v PEG4000, cryoprotection: 4:1 50% PEG3350, 500 mM NaI:reservoir (3 ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å

Detector

Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 10, 2013 / Details: mirrors

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: 1.9→100 Å / Num. all: 44391 / Num. obs: 44391 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / B_iso Wilson estimate: 18.57 Å² / R_merge(I) obs: 0.061 / R_sym value: 0.061 / Χ²: 0.883 / Net I/σ(I): 11

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.9-1.93	5.7	0.585	2177	0.912	1	99.6
1.93-1.97	5.7	0.546	2230	0.912	1	99.8
1.97-2.01	5.7	0.439	2194	0.913	1	100
2.01-2.05	5.7	0.382	2198	0.905	1	99.9
2.05-2.09	5.8	0.328	2224	0.923	1	100
2.09-2.14	5.8	0.294	2203	0.914	1	100
2.14-2.19	5.8	0.253	2231	0.921	1	100
2.19-2.25	5.8	0.202	2220	0.938	1	100
2.25-2.32	5.9	0.185	2206	0.934	1	100
2.32-2.39	5.9	0.154	2223	0.922	1	100
2.39-2.48	5.9	0.133	2193	0.895	1	100
2.48-2.58	5.9	0.113	2239	0.867	1	100
2.58-2.7	6	0.09	2206	0.866	1	100
2.7-2.84	6	0.069	2242	0.857	1	100
2.84-3.02	6	0.056	2201	0.855	1	100
3.02-3.25	6	0.042	2233	0.879	1	100
3.25-3.58	6.1	0.031	2232	0.855	1	100
3.58-4.09	6.1	0.023	2242	0.845	1	100
4.09-5.16	6.1	0.019	2234	0.766	1	100
5.16-100	5.9	0.02	2263	0.797	1	98.6

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
StructureStudio		data collection
HKL-3000		data reduction
HKL-3000	SHELX	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.902→25.637 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8225 / SU ML: 0.24 / σ(F): 0 / σ(I): 0 / Phase error: 25.26 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2476	2230	5.03 %	RANDOM
R_work	0.1855	-	-	-
all	0.1886	44303	-	-
obs	0.1886	44303	99.51 %	-

Solvent computation

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

Displacement parameters

B_iso max: 88.73 Å² / B_iso mean: 25.1889 Å² / B_iso min: 2.84 Å²

Refinement step

Cycle: LAST / Resolution: 1.902→25.637 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4716	0	43	434	5193

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	4847
X-RAY DIFFRACTION	f_angle_d	1.378	6544
X-RAY DIFFRACTION	f_chiral_restr	0.073	705
X-RAY DIFFRACTION	f_plane_restr	0.007	848
X-RAY DIFFRACTION	f_dihedral_angle_d	14.692	1822

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.902-1.9435	0.345	124	0.2541	2440	2564	94
1.9435-1.9887	0.2899	157	0.2276	2613	2770	99
1.9887-2.0384	0.246	155	0.2036	2621	2776	100
2.0384-2.0935	0.2809	119	0.1944	2628	2747	100
2.0935-2.1551	0.2655	128	0.198	2648	2776	100
2.1551-2.2246	0.302	142	0.1956	2632	2774	100
2.2246-2.3041	0.2878	140	0.1946	2656	2796	100
2.3041-2.3963	0.2798	134	0.1875	2623	2757	100
2.3963-2.5053	0.2584	144	0.1935	2635	2779	100
2.5053-2.6372	0.3117	133	0.1946	2631	2764	100
2.6372-2.8023	0.2509	128	0.1926	2670	2798	100
2.8023-3.0183	0.2536	150	0.1973	2618	2768	100
3.0183-3.3215	0.2444	143	0.1919	2667	2810	100
3.3215-3.8008	0.2263	154	0.1642	2640	2794	100
3.8008-4.7835	0.1915	142	0.1428	2642	2784	100
4.7835-25.6396	0.2002	137	0.1858	2709	2846	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	0.0338	-0.0262	0.0135	0.0403	-0.0113	0.0069	0.0671	-0.0271	0.0435	-0.0169	0.0191	-0.0067	-0.0841	0.0652	0.0949	0.0268	-0.1387	0.0271	-0.0441	-0.0226	0.0359	50.8084	32.2657	17.3403
2	0.0078	0.0089	0.0027	0.0108	0.0025	0.003	0.005	0.0094	-0.0197	-0.0161	0.0048	0.0098	0.0009	0.0419	-0.0024	0.042	0.0101	0.0025	0.0951	-0.0315	0.0874	54.0289	20.6439	12.4904
3	0.0193	-0.0025	0.0123	0.0112	0.0117	0.0221	0.0718	0.0103	-0.0719	-0.0164	0.0076	-0.009	0.1035	0.0797	0.0913	-0.0007	0.0951	-0.0861	0.0409	0.0091	0.0331	53.5585	16.0819	29.3056
4	0.0213	0.0131	-0.0267	0.0219	-0.004	0.0363	0.0385	-0.027	-0.0473	0.0118	-0.0011	0.0007	0.0681	-0.0473	0.0473	0.0909	-0.1295	-0.1104	0.0044	-0.0015	0.0669	34.8578	8.5897	24.1102
5	0.0213	-0.0067	-0.0097	0.0376	0.0162	0.01	0.0141	0.0012	0.0058	-0.014	0.0163	-0.0161	0.0014	-0.0101	0.0172	0.2318	-0.0709	-0.0602	0.0832	0.0115	0.1411	33.0409	12.8306	15.4898
6	0.0897	-0.0069	0.0121	0.0669	-0.0194	0.0909	0.0553	0.0051	0.0015	-0.0213	0.0329	-0.0078	0.0342	0.0321	0.105	0.016	-0.0245	0.0099	0.0991	-0.0027	0.0293	41.4043	20.2671	22.8481
7	0.0165	0.0187	-0.0016	0.0317	-0.0026	0.0003	-0.0265	0.0271	0.0073	-0.0139	-0.0058	0.0182	-0.046	0.0486	-0.045	0.0907	-0.1246	0.0002	0.1527	-0.0651	0.0818	59.1725	31.8523	27.1233
8	0.0021	-0.0028	-0.0016	0.0038	0.0017	0.0012	0.0168	-0.0249	0.0206	0.0265	0.0217	-0.0185	0.0067	-0.0746	0	0.0733	-0.0166	0.0098	0.2002	0.0002	0.1087	29.4916	24.1271	33.2895
9	0.0117	-0.0022	0.0014	0.0099	-0.0313	0.0926	0.0446	-0.0016	-0.0408	-0.0102	0.0301	0.0139	0.0737	-0.0308	0.0878	0.3103	-0.0013	-0.1719	0.0584	0.0627	0.1578	41.2693	2.3712	34.4363
10	0.0022	0.0004	0.0012	0.0004	0.0004	0.0003	0.0076	-0.0093	-0.0068	-0.0077	-0.0085	0.0005	0.0167	0.0106	-0.0082	0.1778	0.072	-0.1074	0.1471	0.0073	0.1242	55.4261	8.8455	37.9986
11	0.025	-0.0001	-0.0028	0.0026	-0.0089	0.0333	0.011	-0.0069	-0.0539	0.0101	0.0173	0.0414	0.0277	0.0101	0.002	0.0393	0.0009	0.0054	0.1207	0.0327	0.0772	27.7469	18.8469	-14.593
12	0.138	-0.0442	-0.0682	0.0447	0.0115	0.3319	0.0694	0.064	0.1707	0.0175	0.0824	0.0339	-0.2278	-0.0504	0.1747	0.1005	0.0222	0.043	0.0737	0.0307	0.1014	32.709	35.0923	-9.5915
13	0.0013	0.0013	0.0002	0.0014	0.0002	0.0005	0.0009	0.0096	-0.0021	0.0058	-0.0187	-0.0154	-0.0031	0.0245	0	0.1081	0.0165	0.0289	0.1487	-0.0231	0.1619	48.1353	32.173	-4.7923
14	0.0017	-0.0035	-0.0099	0.0227	0.0396	0.0681	0.0126	0.0212	-0.0426	0.0365	0.0519	0.0435	0.0204	-0.0743	0.0337	0.0241	0.0121	0.0238	0.0974	0.058	0.1511	25.2611	22.4857	-7.8342
15	0.0214	-0.0125	-0.0105	0.0057	0.0038	0.021	0.0388	-0.0174	0.049	0.0602	0.0361	0.0392	-0.0474	0.0564	0.0145	0.2943	0.0607	0.0745	0.1212	-0.0795	0.2608	38.7836	44.1203	2.9312
16	0.0121	0.009	0.0028	0.0294	0.013	0.0055	0.0101	-0.0354	0.0254	0.0404	-0.0031	-0.0069	0.0045	-0.0014	0.0319	0.2353	0.0827	0.1349	0.2166	-0.0328	0.2406	24.6117	38.3916	11.3931

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 29 through 74 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 75 through 93 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 94 through 150 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 151 through 185 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 186 through 203 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 204 through 251 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 252 through 270 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 271 through 295 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 296 through 316 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 317 through 331 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 29 through 57 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 58 through 219 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 220 through 235 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 236 through 288 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 289 through 317 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 318 through 340 )	B

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Jul 12, 2017. Major update of PDB

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Yorodumi