PDB-5ci5: Crystal Structure of an ABC transporter Solute Binding Protein fr...

ID or keywords:

Entry

Database: PDB / ID: 5ci5

Title

Crystal Structure of an ABC transporter Solute Binding Protein from Thermotoga Lettingae TMO (Tlet_1705, TARGET EFI-510544) bound with alpha-D-Tagatose

Components

Extracellular solute-binding protein family 1

Keywords

SUGAR BINDING PROTEIN /

Oxidoreductase /

ENZYME FUNCTION INITIATIVE / EFI /

Structural Genomics

Function / homology

Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta / alpha-D-tagatopyranose / Extracellular solute-binding protein family 1

Function and homology information

Biological species

Pseudothermotoga lettingae

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.61 Å

Authors

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

Citation

Journal: To be published
Title: Crystal Structure of an ABC transporter Solute Binding Protein from Thermotoga Lettingae TMO (Tlet_1705, TARGET EFI-510544) bound with alpha-D-Tagatose
Authors: Yadava, U. / Vetting, M.W. / Al Obaidi, N.F. / Toro, R. / Morisco, L.L. / Benach, J. / Koss, J. / Wasserman, S.R. / Attonito, J.D. / Scott Glenn, A. / Chamala, S. / Chowdhury, S. / Lafleur, ...

History

Deposition	Jul 11, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 22, 2015	Provider: repository / Type: Initial release
Revision 2.0	Nov 15, 2017	Group: Atomic model / Derived calculations / Source and taxonomy Category: atom_site / entity_src_gen / pdbx_struct_oper_list Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 3.0	Jul 29, 2020	Group: Atomic model / Data collection / Derived calculations Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5ci5.cif.gz	466.9 KB	Display	PDBx/mmCIF format
PDB format	pdb5ci5.ent.gz	395.4 KB	Display	PDB format
PDBx/mmJSON format	5ci5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ci/5ci5 ftp://data.pdbj.org/pub/pdb/validation_reports/ci/5ci5	HTTPS FTP

-
Related structure data

Similar structure data	5z6b-d 5dcw-d 6dts-2 5caq-d 5edr-d 1mdp-1 3wsb-2 3wcb-2 4zza-1 4rk9-1 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 - HomologyF&H Search
Other databases	TargetTrack: EFI-510544

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #221 - May 2018 Human Papillomavirus and Vaccines similarity (1) #243 - Mar 2020 Voltage-gated Sodium Channels similarity (1)

Deposited unit

A: Extracellular solute-binding protein family 1

B: Extracellular solute-binding protein family 1

hetero molecules

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

1

A: Extracellular solute-binding protein family 1

hetero molecules

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

2

B: Extracellular solute-binding protein family 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	73.363, 93.077, 103.637
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein

Extracellular solute-binding protein family 1

Mass: 47469.086 Da / Num. of mol.: 2 / Fragment: putative oxidoreductase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudothermotoga lettingae (strain ATCC BAA-301 / DSM 14385 / NBRC 107922 / TMO) (bacteria)
Strain: ATCC BAA-301 / DSM 14385 / NBRC 107922 / TMO / Gene: Tlet_1705 / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8F7X5

#2: Sugar

ChemComp-T6T / alpha-D-tagatopyranose /

Tagatose

Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₂O₆

#3: Chemical

ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL /

Ethylene glycol

Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂

#4: Chemical

ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 /

Polyethylene glycol

Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₂₂O₆ / Comment: precipitant*YM

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1036 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 1.86 Å³/Da / Density % sol: 34 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein (10mM D-tagatose, 10 mM HEPES pH 7.5, 5 mM DTT); Reservoir (0.2 M Sodium chloride, 0.1M Bis-Tris HCl, 25%(w/v) PEG 3350); Cryoprotection (20% Diethylene glycol, 80% Reservoir)

-
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: Jun 26, 2015 / 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: 1.61→50 Å / Num. obs: 92888 / % possible obs: 100 % / Redundancy: 14.7 % / B_iso Wilson estimate: 12.7 Å² / R_merge(I) obs: 0.113 / R_pim(I) all: 0.03 / R_rim(I) all: 0.117 / Χ²: 0.887 / Net I/av σ(I): 23.083 / Net I/σ(I): 6.2 / Num. measured all: 1362797

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
1.61-1.64	14.2	0.957	4569	0.895	0.261	0.992	0.753	100
1.64-1.67	14.3	0.882	4577	0.914	0.24	0.914	0.72	100
1.67-1.7	14.4	0.74	4607	0.933	0.201	0.767	0.727	100
1.7-1.73	14.4	0.665	4592	0.943	0.18	0.689	0.745	100
1.73-1.77	14.5	0.56	4581	0.958	0.151	0.58	0.743	100
1.77-1.81	14.6	0.476	4597	0.969	0.129	0.494	0.734	100
1.81-1.86	14.6	0.4	4616	0.977	0.108	0.415	0.755	100
1.86-1.91	14.7	0.32	4600	0.984	0.086	0.332	0.775	100
1.91-1.97	14.7	0.275	4604	0.987	0.074	0.285	0.864	100
1.97-2.03	14.8	0.231	4623	0.992	0.062	0.239	0.819	100
2.03-2.1	14.9	0.19	4624	0.994	0.051	0.197	0.874	100
2.1-2.19	14.9	0.151	4597	0.995	0.04	0.156	0.756	100
2.19-2.28	14.9	0.144	4666	0.996	0.038	0.149	0.914	100
2.28-2.4	14.9	0.157	4621	0.995	0.042	0.162	1.041	100
2.4-2.56	14.9	0.145	4660	0.994	0.039	0.15	1.173	100
2.56-2.75	15	0.132	4668	0.992	0.035	0.136	1.33	100
2.75-3.03	14.9	0.128	4689	0.994	0.034	0.133	1.594	100
3.03-3.47	14.9	0.094	4707	0.997	0.025	0.097	1.225	100
3.47-4.37	14.8	0.052	4761	0.999	0.014	0.054	0.587	100
4.37-50	14.2	0.052	4929	0.997	0.014	0.054	0.544	99.3

-
Processing

Software

Name	Version	Classification
HKL-2000		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
HKL-3000		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.61→26.619 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.46 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1679	4332	4.91 %
R_work	0.1319	83949	-
obs	0.1337	88281	95.06 %

Solvent computation

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

Displacement parameters

B_iso max: 85.9 Å² / B_iso mean: 18.9239 Å² / B_iso min: 4.3 Å²

Refinement step

Cycle: final / Resolution: 1.61→26.619 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6249	0	96	1043	7388
B_iso mean	-	-	23.82	30.32	-
Num. residues	-	-	-	-	785

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	6530
X-RAY DIFFRACTION	f_angle_d	1.29	8896
X-RAY DIFFRACTION	f_chiral_restr	0.05	950
X-RAY DIFFRACTION	f_plane_restr	0.008	1122
X-RAY DIFFRACTION	f_dihedral_angle_d	13.144	2376

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 (%)
1.6069-1.6252	0.2635	107	0.1865	1947	2054	67
1.6252-1.6443	0.232	101	0.1744	2152	2253	74
1.6443-1.6644	0.2168	146	0.1749	2200	2346	76
1.6644-1.6854	0.2181	103	0.1602	2345	2448	81
1.6854-1.7076	0.2035	141	0.1619	2420	2561	84
1.7076-1.731	0.2149	136	0.1664	2582	2718	88
1.731-1.7557	0.1996	141	0.1651	2646	2787	91
1.7557-1.7819	0.2191	158	0.1648	2729	2887	95
1.7819-1.8097	0.2291	132	0.159	2911	3043	98
1.8097-1.8394	0.1976	137	0.1572	2891	3028	99
1.8394-1.8711	0.1918	132	0.153	2936	3068	100
1.8711-1.9051	0.1974	169	0.1496	2883	3052	100
1.9051-1.9418	0.1681	161	0.1479	2929	3090	100
1.9418-1.9814	0.1819	154	0.1417	2899	3053	100
1.9814-2.0245	0.1808	144	0.1402	2924	3068	100
2.0245-2.0715	0.1771	150	0.1346	2927	3077	100
2.0715-2.1233	0.1599	135	0.1284	2929	3064	100
2.1233-2.1807	0.1486	142	0.1247	2922	3064	100
2.1807-2.2448	0.1756	129	0.1254	2975	3104	100
2.2448-2.3172	0.1578	150	0.1277	2932	3082	100
2.3172-2.4	0.1614	131	0.123	2939	3070	100
2.4-2.496	0.1695	148	0.116	2961	3109	100
2.496-2.6096	0.1497	150	0.1169	2922	3072	100
2.6096-2.747	0.1504	165	0.1231	2967	3132	100
2.747-2.9189	0.1616	173	0.1284	2943	3116	100
2.9189-3.144	0.1814	137	0.1372	2992	3129	100
3.144-3.4597	0.1666	154	0.1267	2982	3136	100
3.4597-3.959	0.1456	167	0.1139	2994	3161	100
3.959-4.9825	0.1215	186	0.1038	3004	3190	100
4.9825-26.6227	0.1735	153	0.1373	3166	3319	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	0.0272	0.0047	-0.0168	0.0229	-0.0075	0.0261	0.0295	0.0258	-0.1124	0.0021	0.0193	-0.0269	0.0901	0.0944	0.0039	0.136	0.0283	-0.0131	0.083	-0.0294	0.1033	68.3172	48.427	70.085
2	0.0312	0.002	0.001	0.0867	-0.0083	0.1393	0.0196	0.0156	-0.0102	-0.027	0.0171	0.0269	0.043	-0.0091	0.0469	0.0623	0.0053	0.0008	0.0667	0.0108	0.0601	60.9404	62.2304	73.128
3	0.0081	0.0046	-0.0027	0.0146	0.011	0.0193	-0.0474	-0.0597	-0.0079	0.066	0.0368	-0.0104	0.0495	-0.039	0.0007	0.0906	0.0197	0.0124	0.1128	0.0175	0.0775	58.711	60.7887	107.2207
4	0.0914	0.0223	-0.0506	0.0878	0.0288	0.1848	0.0128	-0.0102	-0.0075	0.0091	0.0041	-0.0212	-0.0145	-0.0088	0	0.0631	0.0184	-0.0028	0.0554	0.0049	0.0623	63.633	64.3245	91.6252
5	0.0042	-0.001	-0.0043	0.0119	0.0101	0.0093	0.0147	0.0453	-0.1052	-0.0213	-0.052	0.0044	0.0612	-0.0553	-0	0.1421	-0.0131	-0.0055	0.0847	0.0002	0.1147	56.4575	48.492	69.4236
6	0.1023	-0.0845	0.0181	0.0891	0.0523	0.0915	0.013	-0.0252	0.0054	-0.0363	-0.005	-0.0207	-0.0464	-0.0497	0.0096	0.0775	-0.0175	0.0041	0.0749	0.0049	0.0761	60.8779	68.1847	85.0634
7	0.0497	0.0128	-0.0025	0.0558	0.0254	0.0547	-0.0413	0.0896	-0.0271	0.0198	0.071	-0.0422	0.0776	0.1434	-0.0018	0.0822	0.0036	0.0047	0.1152	-0.0207	0.1006	33.6953	50.1858	55.4236
8	-0.0005	-0.0005	-0.0046	0.008	0.0061	0.023	-0.042	0.033	0.016	-0.0443	0.0856	0.0533	-0.0221	0.0628	0.0025	0.0812	-0.0202	0.0006	0.0753	0.0104	0.0638	28.1355	63.253	51.1212
9	0.093	0.0549	-0.0209	0.2108	0.038	0.0205	-0.0123	-0.068	-0.0366	-0.0551	-0.0126	0.0594	-0.007	0.0145	-0.014	0.0366	-0.0043	-0.0024	0.0635	0.0233	0.0609	19.94	58.8776	65.3612
10	0.0092	0.0148	-0.0074	0.0245	-0.0058	0.0099	-0.0128	-0.0885	-0.0008	0.0998	-0.0439	-0.0314	0.0955	-0.0316	-0.0001	0.1608	-0.0317	0.0046	0.2684	0.0082	0.0877	24.7318	59.0056	92.9586
11	0.1104	0.0358	0.014	0.016	0.0293	0.132	-0.0212	-0.16	0.0576	-0.0259	-0.0019	-0.001	-0.0963	-0.0354	-0.0097	0.0714	0.0173	-0.0178	0.0919	-0.0309	0.0743	28.3696	71.8555	78.2548
12	0.2596	0.0784	0.0698	0.0833	0.0297	0.0502	0.0289	-0.0945	-0.0511	-0.0039	0.0056	-0.0431	0.0128	-0.0224	0.0112	0.055	0.005	-0.0112	0.0845	0.0075	0.0877	29.2593	56.662	76.0337
13	0.0461	-0.0106	0.0234	0.0257	0.0169	0.0345	-0.0262	0.0047	-0.0256	-0.0034	0.0001	0.0524	0.0398	-0.0252	-0.0011	0.0864	-0.0125	-0.0009	0.0672	0.0005	0.0844	17.7313	52.9549	62.9045
14	0.006	0.0006	-0.01	0.0112	0.0104	0.0276	-0.1097	-0.0304	0.1594	-0.04	0.0384	-0.0773	-0.0947	0.0342	-0.1081	0.0744	-0.0524	-0.1166	0.0159	-0.0992	0.148	36.2283	78.4049	73.8484

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 19 through 61 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 62 through 147 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 148 through 174 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 175 through 308 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 309 through 332 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 333 through 411 )	A
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 19 through 71 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 72 through 104 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 105 through 148 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 149 through 174 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 175 through 231 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 232 through 308 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 309 through 372 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 373 through 410 )	B

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi