PDB-4pft: Crystal structure of mannobiose bound oligopeptide ABC transporte...

ID or keywords:

Entry

Database: PDB / ID: 4pft

Title

Crystal structure of mannobiose bound oligopeptide ABC transporter, periplasmic oligopeptide-binding protein (TM1223) from THERMOTOGA MARITIMA at 1.75 A resolution

Components

ABC transporter substrate-binding protein

Keywords

TRANSPORT PROTEIN / oligopeptide ABC transporter / periplasmic oligopeptide-binding protein

Function / homology

Function and homology information

peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space /

metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.747 Å

Authors

Lu, X. / Ghimire-Rijal, S. / Cuneo, M.J.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Duplication of Genes in an ATP-binding Cassette Transport System Increases Dynamic Range While Maintaining Ligand Specificity.
Authors: Ghimire-Rijal, S. / Lu, X. / Myles, D.A. / Cuneo, M.J.

History

Deposition	Apr 30, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 17, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 24, 2014	Group: Database references
Revision 1.2	Nov 5, 2014	Group: Database references
Revision 1.3	Feb 4, 2015	Group: Derived calculations
Revision 1.4	Sep 27, 2017	Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_close_contact Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / refine_hist / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_asym.entity_id Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4pft.cif.gz	480.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4pft.ent.gz	390.1 KB	Display	PDB format
PDBx/mmJSON format	4pft.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pf/4pft ftp://data.pdbj.org/pub/pdb/validation_reports/pf/4pft	HTTPS FTP

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Related structure data

Related structure data	4pfuC 4pfwC 4pfyC 1vr5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4pfy-1 4pfu-1 3klp-1 4pfw-1 3n92-d 6lzs-3 5yqw-d 3ryb-d 3drg-d 4pfy-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ABC transporter substrate-binding protein

B: ABC transporter substrate-binding protein

hetero molecules

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

1

A: ABC transporter substrate-binding protein

hetero molecules

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

2

B: ABC transporter substrate-binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.489, 53.540, 106.280
Angle α, β, γ (deg.)	90.00, 110.47, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein

ABC transporter substrate-binding protein / Mannoside ABC transport system / sugar-binding protein / Oligopeptide ABC transporter / periplasmic ...

Mass: 62881.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_1223, THEMA_08215, Tmari_1230 / Production host:

Escherichia coli (E. coli) / References: UniProt: Q9X0V0

#2: Polysaccharide

beta-D-mannopyranose-(1-4)-beta-D-mannopyranose / 4beta-beta-mannobiose

Type: oligosaccharide

, Oligosaccharide

/ Class: Metabolism

/ Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 4beta-beta-mannobiose

#3: Chemical

ChemComp-MG / MAGNESIUM ION

Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

#4: Chemical

ChemComp-NO3 / NITRATE ION /

Nitrate

Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO₃

#5: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 1248 / 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: 2.05 Å³/Da / Density % sol: 39.85 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MgNO3, 20-30% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 18, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.747→50 Å / Num. obs: 103164 / % possible obs: 99.8 % / Redundancy: 3.4 % / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.747→1.8 Å / Redundancy: 3.2 % / R_merge(I) obs: 0.58 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software

Name: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1VR5

1vr5

Resolution: 1.747→46.066 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.65 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2037	5162	5.01 %
R_work	0.1519	-	-
obs	0.1545	103123	99.64 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.747→46.066 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8753	0	60	1248	10061

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9341
X-RAY DIFFRACTION	f_angle_d	1.188	12807
X-RAY DIFFRACTION	f_dihedral_angle_d	12.777	3353
X-RAY DIFFRACTION	f_chiral_restr	0.067	1330
X-RAY DIFFRACTION	f_plane_restr	0.006	1642

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.747-1.767	0.3554	161	0.2823	3055	X-RAY DIFFRACTION	94
1.767-1.7878	0.3188	165	0.2623	3306	X-RAY DIFFRACTION	100
1.7878-1.8096	0.3346	175	0.2456	3211	X-RAY DIFFRACTION	100
1.8096-1.8325	0.2681	198	0.2252	3235	X-RAY DIFFRACTION	100
1.8325-1.8566	0.2499	162	0.2127	3270	X-RAY DIFFRACTION	100
1.8566-1.882	0.2609	149	0.2116	3217	X-RAY DIFFRACTION	100
1.882-1.9089	0.283	183	0.2023	3279	X-RAY DIFFRACTION	100
1.9089-1.9374	0.2828	170	0.1946	3227	X-RAY DIFFRACTION	100
1.9374-1.9677	0.2587	165	0.1885	3274	X-RAY DIFFRACTION	100
1.9677-1.9999	0.2446	187	0.1886	3223	X-RAY DIFFRACTION	100
1.9999-2.0344	0.2521	191	0.1886	3215	X-RAY DIFFRACTION	100
2.0344-2.0714	0.2431	157	0.1769	3247	X-RAY DIFFRACTION	100
2.0714-2.1112	0.2169	179	0.1591	3240	X-RAY DIFFRACTION	100
2.1112-2.1543	0.2009	165	0.1587	3296	X-RAY DIFFRACTION	100
2.1543-2.2012	0.2225	189	0.1586	3232	X-RAY DIFFRACTION	100
2.2012-2.2524	0.2085	158	0.1539	3292	X-RAY DIFFRACTION	100
2.2524-2.3087	0.217	171	0.1481	3234	X-RAY DIFFRACTION	100
2.3087-2.3711	0.194	179	0.1511	3250	X-RAY DIFFRACTION	100
2.3711-2.4409	0.1982	185	0.1454	3282	X-RAY DIFFRACTION	100
2.4409-2.5197	0.1987	174	0.146	3248	X-RAY DIFFRACTION	100
2.5197-2.6097	0.2307	171	0.1518	3287	X-RAY DIFFRACTION	100
2.6097-2.7142	0.2396	171	0.1571	3272	X-RAY DIFFRACTION	100
2.7142-2.8377	0.2252	175	0.1535	3311	X-RAY DIFFRACTION	100
2.8377-2.9873	0.2081	161	0.1505	3267	X-RAY DIFFRACTION	100
2.9873-3.1744	0.1986	178	0.151	3280	X-RAY DIFFRACTION	100
3.1744-3.4194	0.194	184	0.1359	3289	X-RAY DIFFRACTION	100
3.4194-3.7634	0.1559	175	0.1262	3305	X-RAY DIFFRACTION	100
3.7634-4.3076	0.133	164	0.114	3319	X-RAY DIFFRACTION	100
4.3076-5.4258	0.1346	178	0.1062	3351	X-RAY DIFFRACTION	100
5.4258-46.0821	0.191	142	0.1373	3447	X-RAY DIFFRACTION	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	0.8314	0.2917	-0.5653	1.5179	-0.8788	2.5361	-0.0239	0.1105	-0.0581	-0.0398	0.0252	0.1165	0.1004	-0.1864	-0.0061	0.0823	-0.0039	-0.0077	0.1307	-0.0153	0.1326	113.177	102.6513	6.1576
2	0.6957	0.4412	-0.5973	0.9241	-0.9387	1.8674	-0.0405	0.2108	0.0535	-0.1095	0.0975	0.1677	0.0562	-0.2992	-0.0576	0.1216	0.0067	-0.0194	0.1762	-0.013	0.14	113.4784	108.627	-2.1436
3	1.3155	0.65	0.2491	1.261	0.1596	1.1096	-0.0218	0.0115	-0.1018	0.0701	0.026	-0.0146	0.0955	0.1051	0.0075	0.1235	0.0333	0.0102	0.1226	0.0016	0.1011	134.4779	99.0852	15.2994
4	1.4335	0.3696	-0.0954	1.1536	-0.4022	1.7918	-0.065	0.0653	-0.1706	-0.1793	-0.0104	-0.2156	0.191	0.1114	0.019	0.1566	0.0363	0.0071	0.1477	-0.0111	0.1486	142.852	98.468	9.3975
5	0.9756	0.055	0.0966	0.8132	-0.3214	1.2507	-0.003	-0.037	0.1096	0.1387	-0.0313	-0.0244	-0.1529	0.073	0.0356	0.1242	0.0018	-0.0004	0.086	-0.0056	0.1111	137.1565	111.3269	17.6494
6	1.6498	0.7718	-0.0089	1.2815	0.0067	0.9492	-0.0213	0.0745	-0.12	-0.0778	-0.0281	-0.0753	0.0532	0.0194	0.013	0.1206	0.0483	0.0018	0.1108	-0.0177	0.1048	132.606	99.7301	5.7503
7	2.0867	0.2442	0.4161	1.8044	0.1797	2.1271	0.0091	0.1334	-0.2211	-0.0616	0.0257	0.1521	0.3719	-0.0892	-0.015	0.1748	-0.0038	-0.0017	0.1672	-0.0208	0.1622	117.1452	92.301	1.4183
8	0.5233	-0.1241	-0.1626	0.9587	0.7878	1.5422	0.0037	-0.081	0.018	0.053	0.0389	-0.1042	-0.0424	0.1099	-0.0474	0.1019	-0.0117	-0.0152	0.1073	0.0033	0.123	109.123	107.0323	51.6385
9	1.9932	-1.3953	0.5221	2.664	-0.7374	1.1393	-0.0145	0.0027	-0.0604	-0.1495	0.0634	0.1551	0.0847	-0.1178	-0.0562	0.0995	-0.0593	-0.0083	0.1135	-0.0076	0.0777	89.0788	98.5708	34.7888
10	2.1279	-0.8413	-0.4495	1.7372	0.6515	2.7495	-0.0904	-0.0417	-0.1738	0.0239	0.0268	0.3821	0.1689	-0.2258	0.076	0.1313	-0.0653	-0.0068	0.1279	0.0399	0.2049	80.3899	97.7414	39.4631
11	3.0201	-0.3503	0.5389	1.5079	-0.1293	1.6605	-0.0548	0.4406	0.2953	-0.3815	-0.0166	0.253	-0.155	-0.2583	0.0495	0.229	-0.0168	-0.0707	0.2335	0.0375	0.1857	81.4879	107.3801	21.2517
12	1.4299	-0.6238	0.0732	1.3707	-0.1388	0.5697	-0.0058	-0.0842	0.1451	0.0356	0.0517	0.0464	-0.0692	-0.0438	-0.0391	0.0921	-0.0239	0.0022	0.1007	-0.023	0.1125	90.708	108.4277	40.8799
13	3.7277	0.4667	0.471	2.1658	-0.6409	3.7697	0.0748	-0.1629	-0.2225	0.1033	-0.0786	-0.1003	0.3868	0.1085	0.0175	0.1233	0.0059	-0.0108	0.0947	-0.0109	0.1	105.4412	92.1802	49.7181

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 22 through 69 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 70 through 252 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 253 through 301 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 302 through 347 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 348 through 485 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 486 through 528 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 529 through 558 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 21 through 252 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 253 through 301 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 302 through 347 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 348 through 404 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 405 through 528 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 529 through 558 )

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