PDB-8t9t: Apo Crystal Structure of a Substrate Binding Protein (IseP) from ...

ID or keywords:

Entry

Database: PDB / ID: 8t9t

Title

Apo Crystal Structure of a Substrate Binding Protein (IseP) from an Isethionate TRAP Transporter

Components

Isethionate-binding periplasmic protein DctP

Keywords

TRANSPORT PROTEIN / Substrate binding protein / TRAP transporter / Isethionate

Function / homology

C4-dicarboxylate transport / alkanesulfonate catabolic process / TRAP transporter solute receptor, DctP family / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / transmembrane transport / outer membrane-bounded periplasmic space / Isethionate-binding periplasmic protein DctP

Function and homology information

Biological species

Oleidesulfovibrio alaskensis G20 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.48 Å

Authors

Newton-Vesty, M.C. / Dobson, R.C.J.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: Isethionate TRAP transporter substrate binding protein structure and function
Authors: Newton-Vesty, M.C. / Dobson, R.C.J.

History

Deposition	Jun 25, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 26, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8t9t.cif.gz	148 KB	Display	PDBx/mmCIF format
PDB format	pdb8t9t.ent.gz	112.9 KB	Display	PDB format
PDBx/mmJSON format	8t9t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8t9t_validation.pdf.gz	437.1 KB	Display	wwPDB validaton report
Full document	8t9t_full_validation.pdf.gz	440.2 KB	Display
Data in XML	8t9t_validation.xml.gz	18.2 KB	Display
Data in CIF	8t9t_validation.cif.gz	27.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/t9/8t9t ftp://data.pdbj.org/pub/pdb/validation_reports/t9/8t9t	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Isethionate-binding periplasmic protein DctP

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS

Unit cell

Length a, b, c (Å)	42.925, 72.997, 95.24
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Isethionate-binding periplasmic protein DctP / TRAP transporter / DctP solute-binding subunit Mass: 37287.664 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oleidesulfovibrio alaskensis G20 (bacteria) Gene: dctP, Dde_1275 / Production host: Escherichia coli (E. coli) / References: UniProt: Q312S0
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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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 Å³/Da / Density % sol: 38.53 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: Sodium bromide, Bis-Tris propane, PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

Australian Synchrotron

/ Beamline: MX2 / Wavelength: 0.95372 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 8, 2022

Radiation

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

Radiation wavelength

Wavelength: 0.95372 Å / Relative weight: 1

Reflection

Resolution: 1.48→47.665 Å / Num. obs: 50754 / % possible obs: 100 % / Redundancy: 19.8 % / CC_1/2: 0.999 / R_merge(I) obs: 0.066 / R_pim(I) all: 0.021 / R_rim(I) all: 0.07 / Net I/σ(I): 25.6

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all
8.11-47.62	16	0.064	377	0.994	0.022	0.068
1.48-1.51	20.5	0.539	2453	0.975	0.174	0.566

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0425	refinement
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.48→47.665 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.959 / SU B: 1.248 / SU ML: 0.048 / Cross valid method: NONE / ESU R: 0.073 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.203	2541	5.013 %
R_work	0.17	48143	-
all	0.172	-	-
obs	-	50684	99.984 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 23 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.288 Å²	0 Å²	0 Å²
2-	-	-0.181 Å²	0 Å²
3-	-	-	-1.107 Å²

Refinement step

Cycle: LAST / Resolution: 1.48→47.665 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2404	0	18	393	2815

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.012	2619
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	2521
X-RAY DIFFRACTION	r_angle_refined_deg	2.018	1.85	3564
X-RAY DIFFRACTION	r_angle_other_deg	0.683	1.773	5839
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.63	5	346
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.687	5	13
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.445	10	486
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.249	10	118
X-RAY DIFFRACTION	r_chiral_restr	0.105	0.2	398
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3102
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	564
X-RAY DIFFRACTION	r_nbd_refined	0.255	0.2	631
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	2317
X-RAY DIFFRACTION	r_nbtor_refined	0.184	0.2	1282
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	1348
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.214	0.2	273
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.192	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.247	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.236	0.2	77
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.186	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	1.705	2.001	1296
X-RAY DIFFRACTION	r_mcbond_other	1.701	2	1296
X-RAY DIFFRACTION	r_mcangle_it	2.317	3.593	1637
X-RAY DIFFRACTION	r_mcangle_other	2.329	3.595	1638
X-RAY DIFFRACTION	r_scbond_it	3.164	2.362	1323
X-RAY DIFFRACTION	r_scbond_other	3.164	2.363	1324
X-RAY DIFFRACTION	r_scangle_it	4.608	4.173	1914
X-RAY DIFFRACTION	r_scangle_other	4.607	4.174	1915
X-RAY DIFFRACTION	r_lrange_it	5.651	25.169	3255
X-RAY DIFFRACTION	r_lrange_other	5.582	22.298	3142

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.48-1.518	0.229	206	0.203	3485	0.205	3691	0.966	0.971	100	0.182
1.518-1.56	0.232	186	0.196	3404	0.198	3590	0.963	0.973	100	0.177
1.56-1.605	0.216	149	0.181	3358	0.182	3509	0.966	0.977	99.943	0.163
1.605-1.654	0.216	151	0.175	3268	0.177	3419	0.969	0.979	100	0.157
1.654-1.709	0.245	170	0.175	3118	0.179	3289	0.962	0.98	99.9696	0.16
1.709-1.769	0.211	152	0.173	3050	0.175	3202	0.972	0.981	100	0.159
1.769-1.835	0.223	152	0.168	2925	0.171	3077	0.968	0.982	100	0.156
1.835-1.91	0.214	169	0.169	2828	0.171	2997	0.972	0.982	100	0.161
1.91-1.995	0.204	154	0.173	2696	0.175	2850	0.977	0.981	100	0.169
1.995-2.092	0.192	153	0.172	2596	0.173	2749	0.977	0.981	100	0.171
2.092-2.205	0.201	110	0.164	2509	0.165	2620	0.973	0.984	99.9618	0.168
2.205-2.338	0.172	119	0.157	2355	0.158	2474	0.983	0.985	100	0.166
2.338-2.499	0.186	118	0.159	2240	0.16	2358	0.977	0.984	100	0.174
2.499-2.699	0.218	109	0.166	2071	0.169	2180	0.974	0.982	100	0.185
2.699-2.956	0.208	105	0.178	1906	0.18	2011	0.972	0.98	100	0.204
2.956-3.303	0.207	95	0.17	1758	0.172	1853	0.975	0.981	100	0.195
3.303-3.811	0.189	70	0.168	1553	0.169	1623	0.979	0.983	100	0.2
3.811-4.66	0.189	70	0.156	1335	0.158	1405	0.978	0.984	100	0.197
4.66-6.559	0.245	68	0.183	1050	0.186	1119	0.97	0.982	99.9106	0.238
6.559-47.665	0.165	35	0.181	638	0.18	675	0.981	0.979	99.7037	0.237

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