PDB-4x8r: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR...

ID or keywords:

Entry

Database: PDB / ID: 4x8r

Title

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM Rhodobacter sphaeroides (Rsph17029_2138, TARGET EFI-510205) WITH BOUND Glucuronate

Components

TRAP dicarboxylate transporter, DctP subunit

Keywords

SOLUTE-BINDING PROTEIN / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

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

Biological species

Rhodobacter sphaeroides (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.9 Å

Authors

Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. ...

Citation

Journal: To be published
Title: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM Rhodobacter sphaeroides (Rsph17029_2138, TARGET EFI-510205) WITH BOUND Glucuronate
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, J. / Love, ...

History

Deposition	Dec 10, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 2015	Group: Derived calculations
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4x8r.cif.gz	349.6 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4x8r_validation.pdf.gz	462.8 KB	Display	wwPDB validaton report
Full document	4x8r_full_validation.pdf.gz	464.3 KB	Display
Data in XML	4x8r_validation.xml.gz	29 KB	Display
Data in CIF	4x8r_validation.cif.gz	44.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x8/4x8r ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x8r	HTTPS FTP

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Related structure data

Similar structure data	4n8y-2 4pbq-1 4mni-d 5i7i-1 2pfy-2 5iga-d 4o7m-4 5i5p-2 4p9k-d 4xeq-4 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-510205

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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

75.7 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
37.8 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
37.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.800, 116.800, 111.937
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	A-542- HOH

Details

biological unit is a Monomer

#1: Protein

TRAP dicarboxylate transporter, DctP subunit

Mass: 37451.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Rhodobacter sphaeroides (strain ATCC 17029 / ATH 2.4.9) (bacteria)
Strain: ATCC 17029 / ATH 2.4.9 / Gene: Rsph17029_2138 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A3PLM5

#2: Sugar

ChemComp-BDP / beta-D-glucopyranuronic acid / D-GLUCURONIC ACID

Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₀O₇

#3: Chemical

ChemComp-PO4 / PHOSPHATE ION

Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.55 Å³/Da / Density % sol: 51.73 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: Protein (30.12 mg/ml, 10 mM HEPES pH 7.5, 5 mM DTT, 10 mM D-Glucuronate); Reservoir (MCSG 1, F7, 0.1 M Sodium/Potassium phosphate pH 5.6

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.97931 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 12, 2014 / Details: MIRRORS

Radiation

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

Radiation wavelength

Wavelength: 0.97931 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 84879 / % possible obs: 99.1 % / Redundancy: 15.5 % / B_iso Wilson estimate: 15.31 Å² / R_merge(I) obs: 0.141 / Χ²: 0.984 / Net I/av σ(I): 16.827 / Net I/σ(I): 5.5 / Num. measured all: 1314798

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	Num. unique all	Χ²	% possible all	R_merge(I) obs
1.7-1.73	12.5	3525	0.912	83.3
1.73-1.76	14.3	4208	0.918	100
1.76-1.79	14.7	4219	0.941	100
1.79-1.83	14.9	4219	0.944	100
1.83-1.87	15	4231	0.965	100
1.87-1.91	15.1	4225	0.994	100
1.91-1.96	15.3	4231	1.019	100	0.765
1.96-2.02	15.4	4248	0.99	100	0.836
2.02-2.07	15.5	4243	0.969	100	0.592
2.07-2.14	15.6	4244	0.967	100	0.46
2.14-2.22	15.6	4262	0.968	100	0.405
2.22-2.31	15.8	4221	1.04	100	0.285
2.31-2.41	15.9	4272	0.913	100	0.256
2.41-2.54	16	4292	0.878	100	0.198
2.54-2.7	16.3	4289	0.84	100	0.169
2.7-2.91	16.5	4291	0.87	100	0.139
2.91-3.2	16.5	4322	1.29	100	0.14
3.2-3.66	16.4	4341	1.672	100	0.13
3.66-4.61	16.3	4398	0.91	100	0.075
4.61-50	15.5	4598	0.629	99.2	0.056

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Processing

Software

Name	Version	Classification
HKL-2000		data reduction
PHENIX	(phenix.refine: 1.9_1692)	refinement
PDB_EXTRACT	3.15	data extraction

Refinement

Resolution: 1.9→25.434 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.43 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2013	2951	4.83 %
R_work	0.1566	58156	-
obs	0.1587	61107	99.53 %

Solvent computation

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

Displacement parameters

B_iso max: 107.18 Å² / B_iso mean: 22.217 Å² / B_iso min: 3.32 Å²

Refinement step

Cycle: final / Resolution: 1.9→25.434 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4804	0	64	589	5457
B_iso mean	-	-	29.81	32.43	-
Num. residues	-	-	-	-	608

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4964
X-RAY DIFFRACTION	f_angle_d	1.264	6724
X-RAY DIFFRACTION	f_chiral_restr	0.051	732
X-RAY DIFFRACTION	f_plane_restr	0.006	882
X-RAY DIFFRACTION	f_dihedral_angle_d	14.898	1852

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.9-1.9312	0.2567	138	0.247	2576	2714	94
1.9312-1.9645	0.2623	139	0.2211	2670	2809	98
1.9645-2.0002	0.2416	124	0.1952	2734	2858	99
2.0002-2.0386	0.2217	152	0.1709	2709	2861	100
2.0386-2.0802	0.2263	143	0.1606	2740	2883	100
2.0802-2.1254	0.1839	162	0.1529	2741	2903	100
2.1254-2.1748	0.2204	157	0.1541	2718	2875	100
2.1748-2.2292	0.225	134	0.1647	2737	2871	100
2.2292-2.2894	0.2671	157	0.2025	2755	2912	100
2.2894-2.3568	0.1825	136	0.1592	2749	2885	100
2.3568-2.4328	0.1819	147	0.1367	2769	2916	100
2.4328-2.5196	0.1858	138	0.1303	2759	2897	100
2.5196-2.6204	0.1971	130	0.1363	2775	2905	100
2.6204-2.7396	0.1976	117	0.1427	2795	2912	100
2.7396-2.8838	0.1798	117	0.1508	2793	2910	100
2.8838-3.0642	0.2221	148	0.1587	2800	2948	100
3.0642-3.3003	0.2233	139	0.1653	2806	2945	100
3.3003-3.6316	0.1965	135	0.1472	2807	2942	100
3.6316-4.1551	0.1788	140	0.1349	2845	2985	100
4.1551-5.2275	0.1419	122	0.1209	2888	3010	100
5.2275-25.4364	0.1879	176	0.1771	2990	3166	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	0.0131	-0.0037	0.005	0.0237	-0.0314	0.0422	0.0045	-0.0096	0.009	0.0306	-0.0141	0.0054	-0.0137	0.0199	-0.0248	0.1276	-0.0208	0.0606	0.0504	-0.0078	0.065	9.5594	46.7112	52.5641
2	0.0017	0.0019	0.0013	0.0022	0.0015	0.0013	0.0015	-0.001	0.0035	0.0021	-0.0002	0.0031	-0.0054	0.0076	0.005	0.071	-0.0277	0.0372	0.0796	0.0278	0.0617	15.5419	44.1092	37.5793
3	0.0265	0.0106	-0.0111	0.0155	0.0196	0.0594	0.0095	-0.0076	0.0019	0.0111	0.0088	0.006	-0.0045	0.0405	0.0457	0.0474	0.0165	0.0323	0.0557	0.0213	0.0415	13.7762	27.8641	42.9901
4	0.006	0.0143	-0.0118	0.047	-0.0259	0.0209	-0.0108	0.0378	0.0131	-0.0335	0.0516	0.0624	0.0118	-0.0208	0.0699	-0.0118	-0.0428	0.0295	0.0485	0.0749	0.0384	4.1282	32.6836	31.5342
5	0.0071	0.0011	-0.0099	0.0234	-0.0135	0.0188	0.0064	0.0016	0	0.0377	-0.0149	0.0297	-0.0153	-0.0039	-0.0115	0.0615	-0.0041	0.0439	0.0726	0.0155	0.0626	2.4331	36.1454	50.5717
6	0.0054	0.0009	0.0017	0.0012	0.0038	0.0213	-0.004	0.0088	-0.0046	-0.0029	0.0222	0.0091	0.0398	-0.0066	0.0118	0.1203	-0.0027	0.0374	0.0981	0.0042	0.1647	1.0501	19.1427	29.3229
7	0.001	0.001	-0.0002	0.0012	-0.0002	0	0.0059	0.0035	-0.0057	0.0128	0.0002	0.0024	0.0093	0.0083	0	0.184	0.112	0.0225	0.175	0.0507	0.1748	16.2886	14.7154	41.7607
8	0.0007	0.0004	0.001	0.0005	-0.0018	0.0122	-0.0017	0.0126	0.009	-0.01	-0.0024	0.0049	0.0036	-0.0049	-0.0167	0.0417	-0.0169	-0.0274	0.0804	0.0461	0.0606	11.9635	52.4451	8.0857
9	0.0011	0.0002	0.0004	0.003	0.0018	0.0058	-0.0114	0.0092	0.0034	-0.0079	0.0048	0.0169	0.0122	-0.0101	-0.0093	0.0479	-0.0369	-0.0101	0.085	0.0387	0.0629	11.3044	46.2029	14.8416
10	0.0006	0.0002	0.0009	0.0024	0.0025	0.0037	0.0029	0.0178	-0.0034	-0.0179	-0.0073	-0.0152	0.0393	0.0142	0.0083	0.0479	0.0048	0.0064	0.0785	0.051	0.0637	29.2354	44.1304	14.6083
11	0.0037	0.0047	-0.0092	0.0086	-0.0066	0.0251	0.0205	-0.0495	0.0105	0.0323	-0.0278	-0.0216	-0.0161	0.0496	0.0045	0.0442	-0.0614	-0.0045	0.0766	0.0479	0.0264	27.3697	53.5206	27.1193
12	0.002	0.0034	-0.005	0.0043	-0.0074	0.0104	-0.0156	0.0231	0.021	0.0009	-0.0107	-0.0159	-0.0004	0.0211	-0.0348	0.0848	-0.0364	-0.0333	0.0795	0.0576	0.0659	22.3145	57.2232	8.679
13	0.0008	-0.0007	-0.0007	0.0004	0.0002	0.001	-0.0069	-0.0011	-0.0035	0.007	-0.0094	-0.0083	-0.0149	0.0378	-0.0004	0.0852	-0.0132	-0.0057	0.1433	0.0638	0.1614	41.1619	54.8148	28.1837
14	0.0016	0.0018	-0.0004	0.0025	0	0.0028	0.0083	0.0079	-0.004	-0.0032	0.0022	-0.0046	0.0011	0.0039	0.0023	0.0995	0.0699	0.0292	0.1814	0.0602	0.162	42.0886	39.9884	14.1525

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 63 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 80 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 81 through 134 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 135 through 248 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 249 through 284 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 285 through 308 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 309 through 325 )	A
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 22 through 53 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 54 through 79 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 80 through 134 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 135 through 248 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 249 through 284 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 285 through 308 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 309 through 325 )	B

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