PDB-5cm6: CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FR...

ID or keywords:

Entry

Database: PDB / ID: 5cm6

Title

CRYSTAL STRUCTURE OF A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM PSEUDOALTEROMONAS ATLANTICA T6c(Patl_2292, TARGET EFI-510180) WITH BOUND SODIUM AND PYRUVATE

Components

TRAP dicarboxylate transporter-DctP subunit

Keywords

TRANSPORT PROTEIN / Solute binding protein / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

tripartite ATP-independent periplasmic transporter complex / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function

Biological species

Pseudoalteromonas atlantica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.83 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 PSEUDOALTEROMONAS ATLANTICA T6c(Patl_2292, TARGET EFI-510180) WITH BOUND SODIUM AND PYRUVATE
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	Jul 16, 2015	Deposition site: RCSB / Processing site: RCSB
Supersession	Jul 29, 2015	ID: 4X26
Revision 1.0	Jul 29, 2015	Provider: repository / Type: Initial release
Revision 2.0	Nov 15, 2023	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5cm6.cif.gz	399.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5cm6.ent.gz	332.9 KB	Display	PDB format
PDBx/mmJSON format	5cm6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cm/5cm6 ftp://data.pdbj.org/pub/pdb/validation_reports/cm/5cm6	HTTPS FTP

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Related structure data

Similar structure data	3wxz-d 5gk1-1 6j1m-d 4gqn-d 2hzk-2 3wy0-d 4pet-d 2g59-d 1cxh-d 3bk7-d 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-510180

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: TRAP dicarboxylate transporter-DctP subunit

B: TRAP dicarboxylate transporter-DctP subunit

hetero molecules

83.3 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)	83.345, 83.345, 198.082
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	TRAP dicarboxylate transporter-DctP subunit Mass: 41519.242 Da / Num. of mol.: 2 / Fragment: solute binding protein (UNP residues 23-357) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas atlantica (bacteria) / Strain: T6c / ATCC BAA-1087 / Gene: Patl_2292 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15TH9
#2: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₄O₃
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 521 / 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: 2.07 Å³/Da / Density % sol: 40.62 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein (40.2 mg/ml, 20 mM TRIS pH 8.0, 5 mM DTT, 150 mM NaCl, 5% Glycerol, 10 mM Pyruvate, 1 mM CaCl2); Reservoir (0.2 M Ammonium fluoride, 20 %(w/v) PEG 3350); Cryoprotection (80% ...Details: Protein (40.2 mg/ml, 20 mM TRIS pH 8.0, 5 mM DTT, 150 mM NaCl, 5% Glycerol, 10 mM Pyruvate, 1 mM CaCl2); Reservoir (0.2 M Ammonium fluoride, 20 %(w/v) PEG 3350); Cryoprotection (80% Reservoir,20% ethylene glycol)

Crystal

Density Matthews: 2.07 Å³/Da / Density % sol: 40.62 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Protein (40.2 mg/ml, 20 mM TRIS pH 8.0, 5 mM DTT, 150 mM NaCl, 5% Glycerol, 10 mM Pyruvate, 1 mM CaCl2); Reservoir (0.2 M Ammonium fluoride, 20 %(w/v) PEG 3350); Cryoprotection (80% ...

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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 MX225HE / Detector: CCD / Date: Jun 26, 2015 / 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: 1.83→20 Å / Num. obs: 62371 / % possible obs: 99.8 % / Redundancy: 14.4 % / B_iso Wilson estimate: 20.82 Å² / R_merge(I) obs: 0.1 / R_pim(I) all: 0.028 / R_rim(I) all: 0.103 / Χ²: 0.938 / Net I/av σ(I): 24.684 / Net I/σ(I): 6.1 / Num. measured all: 898089

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	Num. unique all	CC_1/2	Χ²	% possible all	R_merge(I) obs	R_pim(I) all	R_rim(I) all
1.83-1.86	12.3	3010	0.415	0.774	97.9
1.86-1.9	14.3	3073	0.603	0.823	99.9
1.9-1.93	14.5	3051	0.762	1.174	100	0.958	0.257	0.992
1.93-1.97	14.5	3071	0.787	0.843	100		0.59
1.97-2.01	14.6	3051	0.863	0.844	100		0.318
2.01-2.06	14.6	3089	0.916	0.854	100	0.81	0.217	0.839
2.06-2.11	14.6	3079	0.928	0.872	100	0.672	0.179	0.695
2.11-2.17	14.7	3088	0.956	0.891	100	0.573	0.153	0.594
2.17-2.23	14.7	3098	0.967	0.926	100	0.602	0.161	0.623
2.23-2.31	14.6	3097	0.964	1.466	100	0.413	0.111	0.428
2.31-2.39	14.7	3101	0.988	0.858	100	0.284	0.076	0.294
2.39-2.48	14.8	3086	0.99	0.848	100	0.227	0.061	0.235
2.48-2.6	14.7	3120	0.994	0.828	100	0.172	0.046	0.178
2.6-2.73	14.7	3097	0.995	0.794	100	0.139	0.037	0.144
2.73-2.9	14.7	3139	0.997	0.756	100	0.11	0.029	0.113
2.9-3.13	14.6	3154	0.997	0.843	100	0.098	0.026	0.102
3.13-3.44	14.6	3151	0.995	1.34	100	0.106	0.029	0.11
3.44-3.93	14.1	3201	0.995	1.774	100	0.108	0.029	0.112
3.93-4.94	14.3	3235	0.998	0.846	100	0.063	0.017	0.066
4.94-20	13.4	3380	0.999	0.39	98.5	0.04	0.011	0.041

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Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX	(phenix.refine: 1.9_1692)	refinement
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
PHENIX		phasing

Refinement

Resolution: 1.83→19.966 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.15 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2432	2919	4.92 %
R_work	0.1842	56402	-
obs	0.1872	59321	95.37 %

Solvent computation

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

Displacement parameters

B_iso max: 109.65 Å² / B_iso mean: 30.5671 Å² / B_iso min: 6.31 Å²

Refinement step

Cycle: final / Resolution: 1.83→19.966 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5290	0	20	535	5845
B_iso mean	-	-	21.56	32.73	-
Num. residues	-	-	-	-	660

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	5454
X-RAY DIFFRACTION	f_angle_d	1.329	7370
X-RAY DIFFRACTION	f_chiral_restr	0.053	757
X-RAY DIFFRACTION	f_plane_restr	0.007	948
X-RAY DIFFRACTION	f_dihedral_angle_d	14.851	2004

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 (%)
1.83-1.8619	0.3767	75	0.3081	1281	1356	46
1.8619-1.894	0.5744	105	0.4459	1939	2044	70
1.894-1.9284	0.4718	142	0.3895	2477	2619	90
1.9284-1.9654	0.3615	142	0.2963	2715	2857	98
1.9654-2.0055	0.316	136	0.2409	2770	2906	100
2.0055-2.0491	0.2827	135	0.2087	2772	2907	100
2.0491-2.0967	0.262	150	0.1986	2785	2935	100
2.0967-2.1491	0.2727	157	0.1954	2750	2907	100
2.1491-2.2071	0.2449	126	0.2147	2797	2923	100
2.2071-2.272	0.3085	158	0.25	2790	2948	100
2.272-2.3452	0.274	139	0.2103	2768	2907	99
2.3452-2.4289	0.2412	132	0.1739	2813	2945	100
2.4289-2.5259	0.2398	157	0.1601	2791	2948	100
2.5259-2.6406	0.2085	124	0.1605	2829	2953	100
2.6406-2.7795	0.217	169	0.1513	2811	2980	100
2.7795-2.9532	0.2344	152	0.1716	2809	2961	100
2.9532-3.1803	0.25	141	0.1794	2826	2967	100
3.1803-3.4988	0.215	157	0.1642	2855	3012	100
3.4988-4.0016	0.2075	124	0.1514	2871	2995	99
4.0016-5.0282	0.1668	164	0.1315	2891	3055	100
5.0282-19.9667	0.2208	134	0.1738	3062	3196	99

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	0.0249	0.0046	0.0217	0.0462	0.057	0.0881	0.0563	0.0837	0.1213	-0.0753	0.0985	-0.0329	-0.1242	-0.0248	0.0535	0.2217	0.0164	0.0741	0.0746	0.0663	0.2147	-3.8852	67.6183	16.0631
2	0.0109	-0.0017	0.0043	0.0111	0.004	0.0041	-0.0001	0.1655	0.0426	-0.0121	0.043	0.0353	-0.0452	-0.1608	0.0156	0.0693	0.0545	-0.0624	0.2383	0.0633	0.0109	-15.7738	52.8314	19.5748
3	0.0018	0.001	0.0006	0.0016	0.0018	0.0013	-0.0118	-0.0267	0.0137	0.0433	0.0459	0.0391	0.0166	-0.0142	-0.0003	0.1784	0.0728	0.0043	0.1457	0.0204	0.1168	-18.7977	55.7348	44.9093
4	0.0774	-0.0257	-0.0245	0.0505	0.0264	0.0145	-0.0107	0.09	0.1506	-0.0205	0.0149	-0.0439	-0.0666	-0.0371	0.0305	0.0821	0.1014	-0.0312	0.1326	0.0299	0.123	-12.1894	59.7584	32.5446
5	0.0061	0.0072	-0.0046	0.0316	0.0021	0.0139	0.0169	0.0019	0.048	-0.037	0.1157	-0.0904	-0.0014	0.0141	0.0301	0.0562	0.0056	-0.0325	0.1309	-0.0288	0.089	0.1088	53.5273	21.3035
6	0.0135	-0.0143	-0.0184	0.0081	0.0147	0.0202	0.0338	0.0176	-0.0064	0.137	0.0695	0.0014	0.0153	-0.0124	-0	0.1422	0.0386	-0.0447	0.1974	0.0299	0.1207	-18.975	47.827	38.2986
7	0.0281	-0.0082	-0.0007	0.0254	0.0186	0.0198	-0.0694	0.0387	-0.0434	0.048	0.003	-0.0272	0.0783	-0.0861	-0.0044	0.0972	0.0088	-0.0186	0.1761	0.0065	0.1072	-12.9316	36.045	25.1358
8	0.0062	-0.0061	-0.0003	0.0304	-0.0103	0.0049	0.0097	0.0092	0.0044	-0.0146	0.0294	-0.0024	-0.0208	-0.0052	0.0522	0.1159	-0.1753	0.0343	0.2357	-0.0861	0.1228	5.0347	43.1443	0.6899
9	0.1291	-0.0161	0.0025	0.2285	0.0912	0.1338	-0.089	0.0905	-0.099	-0.0405	0.2281	-0.1671	0.1034	0.1399	0.0981	0.0874	-0.0409	-0.004	0.1496	-0.1264	0.2033	11.6516	34.412	13.9286
10	0.0027	-0.0035	-0.0009	0.0038	0.0003	0.001	-0.02	0.0232	-0.013	-0.006	0.0175	-0.0294	0.0212	0.0043	-0	0.22	0.0945	-0.0583	0.2373	-0.0901	0.3202	10.8021	19.501	15.4351
11	0.001	-0.0059	0.0139	0.003	0.0057	0.0174	-0.0303	0.0414	-0.0583	-0.023	0.1319	-0.1411	0.0886	0.0907	0.0628	-0.0428	-0.1896	-0.0879	-0.0206	-0.1171	0.0792	2.3757	33.2082	12.1252
12	0.0039	-0.0033	-0.0019	0.0106	-0.0038	0.0041	-0.0058	0.0071	0.0054	-0.0018	0.0645	-0.0348	0.1303	-0.0045	0.0001	0.2396	0.0459	-0.0864	0.1558	-0.0063	0.2769	7.5843	22.6516	28.7252
13	0.0219	-0.0304	0.0605	0.1334	-0.1163	0.1732	0.0228	-0.0171	-0.0537	0.0396	0.0764	-0.0481	0.0282	0.0195	0.1365	0.0449	0.1272	-0.1286	0.1016	-0.0386	0.0915	4.6285	40.18	32.7397

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 26:92 )	A	26 - 92
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 93:154 )	A	93 - 154
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 155:175 )	A	155 - 175
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 176:253 )	A	176 - 253
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 254:287 )	A	254 - 287
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 288:321 )	A	288 - 321
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 322:356 )	A	322 - 356
8	X-RAY DIFFRACTION	8	( CHAIN B AND ( RESID 26:56 OR RESID 57:57 ) )	B	26 - 56
9	X-RAY DIFFRACTION	8	( CHAIN B AND ( RESID 26:56 OR RESID 57:57 ) )	B	57
10	X-RAY DIFFRACTION	9	( CHAIN B AND RESID 58:175 )	B	58 - 175
11	X-RAY DIFFRACTION	10	( CHAIN B AND RESID 176:202 )	B	176 - 202
12	X-RAY DIFFRACTION	11	( CHAIN B AND RESID 203:289 )	B	203 - 289
13	X-RAY DIFFRACTION	12	( CHAIN B AND RESID 290:321 )	B	290 - 321
14	X-RAY DIFFRACTION	13	( CHAIN B AND RESID 322:354 )	B	322 - 354

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