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

ID or keywords:

Entry

Database: PDB / ID: 4pfu

Title

Crystal structure of mannobiose bound oligopeptide ABC transporter, periplasmic oligopeptide-binding protein (TM1226) from THERMOTOGA MARITIMA at 2.05 A resolution

Components

ABC transporter substrate-binding protein

Keywords

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

Function / homology

Function and homology information

ATP-binding cassette (ABC) transporter complex / transmembrane transport / periplasmic space / metal ion binding
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION / Resolution: 2.049 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	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 1.4	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	Dec 27, 2023	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4pfu.cif.gz	484.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4pfu.ent.gz	396.4 KB	Display	PDB format
PDBx/mmJSON format	4pfu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4pfu_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	4pfu_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4pfu_validation.xml.gz	47.3 KB	Display
Data in CIF	4pfu_validation.cif.gz	71.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pf/4pfu ftp://data.pdbj.org/pub/pdb/validation_reports/pf/4pfu	HTTPS FTP

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Related structure data

Related structure data	4pftC 4pfwC 4pfyC C: citing same article (ref.)
Similar structure data	4pft-2 3drg-d 6lzs-2 4pft-1 4pfw-1 3klp-1 6lzt-d 1fds-1 6lzs-4 4pfy-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 - 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

130 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
65.3 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
65.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	100.911, 193.867, 159.513
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-743- HOH

#1: Protein

ABC transporter substrate-binding protein / Mannoside ABC transport system / sugar-binding protein

Mass: 63835.129 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: THEMA_08200, Tmari_1233 / Production host:

Escherichia coli (E. coli) / References: UniProt: G4FEC0

#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-SO4 / SULFATE ION

Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 813 / 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: 3.06 Å³/Da / Density % sol: 59.74 %
Crystal grow	Temperature: 293 K / Method: evaporation / Details: 2.2 M AmSO4, 0.2 M tri-Li Citrate

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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: Mar 12, 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: 2.049→50 Å / Num. obs: 96558 / % possible obs: 98.5 % / Redundancy: 5.7 % / Net I/σ(I): 18.2
Reflection shell	Resolution: 2.049→2.073 Å / Redundancy: 5.3 % / R_merge(I) obs: 0.584 / Mean I/σ(I) obs: 3.5 / % possible all: 96.1

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Processing

Software

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

Refinement

Resolution: 2.049→48.467 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.01 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2081	4824	5 %
R_work	0.1734	-	-
obs	0.1752	96495	98.42 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.049→48.467 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8869	0	148	813	9830

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	9499
X-RAY DIFFRACTION	f_angle_d	1.073	13035
X-RAY DIFFRACTION	f_dihedral_angle_d	12.453	3370
X-RAY DIFFRACTION	f_chiral_restr	0.045	1338
X-RAY DIFFRACTION	f_plane_restr	0.006	1651

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 (%)
2.049-2.0725	0.3053	166	0.2473	2872	X-RAY DIFFRACTION	94
2.0725-2.0969	0.271	137	0.2249	2978	X-RAY DIFFRACTION	96
2.0969-2.1225	0.2515	143	0.2246	2966	X-RAY DIFFRACTION	96
2.1225-2.1494	0.2326	154	0.2124	2972	X-RAY DIFFRACTION	96
2.1494-2.1776	0.2863	166	0.2109	2934	X-RAY DIFFRACTION	97
2.1776-2.2075	0.2623	141	0.2167	2995	X-RAY DIFFRACTION	97
2.2075-2.239	0.2744	157	0.2106	2986	X-RAY DIFFRACTION	96
2.239-2.2724	0.2709	152	0.2018	3015	X-RAY DIFFRACTION	97
2.2724-2.3079	0.2644	139	0.2026	3012	X-RAY DIFFRACTION	98
2.3079-2.3458	0.2797	155	0.197	3000	X-RAY DIFFRACTION	97
2.3458-2.3862	0.2546	172	0.1906	3018	X-RAY DIFFRACTION	99
2.3862-2.4296	0.2418	196	0.1886	3024	X-RAY DIFFRACTION	99
2.4296-2.4763	0.2203	172	0.1892	3019	X-RAY DIFFRACTION	98
2.4763-2.5269	0.246	156	0.1906	3037	X-RAY DIFFRACTION	98
2.5269-2.5818	0.231	172	0.1833	3055	X-RAY DIFFRACTION	99
2.5818-2.6419	0.2304	157	0.1806	3081	X-RAY DIFFRACTION	99
2.6419-2.7079	0.2217	153	0.1778	3071	X-RAY DIFFRACTION	99
2.7079-2.7811	0.2154	185	0.188	3023	X-RAY DIFFRACTION	99
2.7811-2.863	0.2198	153	0.1912	3092	X-RAY DIFFRACTION	99
2.863-2.9554	0.2391	161	0.1873	3128	X-RAY DIFFRACTION	99
2.9554-3.061	0.2419	149	0.195	3067	X-RAY DIFFRACTION	99
3.061-3.1835	0.2451	153	0.179	3105	X-RAY DIFFRACTION	100
3.1835-3.3284	0.2038	165	0.1777	3111	X-RAY DIFFRACTION	100
3.3284-3.5038	0.2184	149	0.167	3111	X-RAY DIFFRACTION	100
3.5038-3.7233	0.1647	152	0.159	3128	X-RAY DIFFRACTION	100
3.7233-4.0106	0.1671	159	0.1419	3126	X-RAY DIFFRACTION	100
4.0106-4.414	0.1684	175	0.1365	3138	X-RAY DIFFRACTION	100
4.414-5.0521	0.1727	155	0.1313	3160	X-RAY DIFFRACTION	100
5.0521-6.3628	0.1743	168	0.1669	3176	X-RAY DIFFRACTION	100
6.3628-48.4803	0.185	212	0.1803	3271	X-RAY DIFFRACTION	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	0.6657	0.8153	0.4986	1.1745	-0.2004	2.6545	0.2984	-0.5266	0.175	0.3194	-0.4699	0.3343	0.2439	-0.6651	0.1778	0.2751	-0.1454	0.0156	0.6791	-0.066	0.3751	-44.2904	-50.8084	25.7754
2	2.5179	0.8096	0.3017	1.5268	0.5718	2.2972	0.2233	-0.5975	0.0205	0.2076	-0.1823	-0.0798	0.2671	-0.3589	-0.0616	0.2114	-0.0395	-0.0256	0.3246	0.0166	0.1929	-22.3606	-45.7985	32.9931
3	2.4713	0.4371	0.2693	1.0175	0.161	2.0599	0.3804	-0.9389	-0.2171	0.4604	-0.2132	-0.0643	0.5119	-0.4339	-0.1205	0.4776	-0.2104	-0.0671	0.6412	0.0672	0.2489	-24.6935	-53.0121	43.2356
4	1.6241	0.4634	0.6431	1.1824	0.7667	1.7727	0.2236	-0.715	0.1373	0.1684	-0.3428	0.2853	0.1888	-0.8094	0.0947	0.2277	-0.1006	0.0366	0.6427	-0.0498	0.2824	-40.4825	-48.2084	28.567
5	1.9322	1.0584	0.1946	3.2062	1.5687	1.5078	0.0745	-0.0493	-0.172	-0.1024	0.0194	-0.032	0.1691	-0.1006	-0.0926	0.1979	-0.04	-0.0406	0.2291	0.0213	0.1568	-31.0192	-60.1852	6.8306
6	2.5596	1.3457	1.4263	2.4872	1.474	2.3941	-0.1337	0.3448	-0.0401	-0.2268	0.1491	-0.3253	0.0409	0.2514	-0.0359	0.3164	0.0074	0.0078	0.2843	0.0516	0.3237	-21.3051	-60.5018	5.3128
7	2.0648	1.2141	0.4647	1.5264	0.6805	1.3222	0.2379	-0.2391	-0.4672	0.3006	-0.0985	-0.2702	0.5867	-0.1153	-0.112	0.3966	-0.0314	-0.1133	0.2449	0.1107	0.3354	-33.0024	-72.6782	11.3676
8	2.2395	0.5412	0.5676	2.4444	0.3751	1.7894	0.3484	-0.3096	-0.523	0.3348	-0.0875	-0.666	0.5797	0.128	-0.2397	0.4076	0.0575	-0.1723	0.3231	0.0831	0.4937	-12.7848	-66.8492	21.6269
9	0.8334	0.5904	0.3249	1.8393	0.808	1.9035	0.0674	-0.3024	0.0995	-0.1032	-0.1075	0.3565	-0.0838	-0.3161	0.0443	0.1524	0.0148	-0.0304	0.3065	-0.019	0.2289	-33.6478	-44.36	15.832
10	0.7346	0.1372	-1.0309	3.6548	1.5139	2.2087	0.0101	0.0053	0.0408	-0.0634	-0.1541	-0.3995	-0.2103	0.2644	0.1732	0.1704	-0.0086	0.0001	0.2367	0.0553	0.2381	2.0044	-25.7741	21.5176
11	0.9351	0.3107	0.5486	0.8558	0.4987	1.4078	-0.0384	-0.1688	0.2516	-0.053	-0.1719	0.3155	-0.4012	-0.4975	0.1625	0.2566	0.1242	-0.0246	0.313	-0.0915	0.3256	-20.707	-18.8142	30.5006
12	0.8718	0.3265	0.0888	0.7533	0.1552	2.4012	-0.0441	0.0311	0.033	-0.1281	-0.0706	-0.0342	-0.0705	0.0844	0.1158	0.1449	0.0279	0.002	0.1396	0.0296	0.1813	-3.9982	-28.3285	19.6231
13	3.0281	-0.0739	-0.5313	1.7275	0.198	2.596	-0.2277	0.284	0.3248	-0.1699	-0.0527	0.1461	-0.32	0.0088	0.2327	0.463	0.0267	-0.0814	0.2278	0.0556	0.3388	-11.888	-19.3717	-8.4403
14	1.7903	-0.4833	0.2328	0.9084	0.1907	2.0231	-0.1856	0.4778	0.4359	-0.6031	-0.0417	0.1217	-0.3712	0.0425	0.208	0.5855	0.0097	-0.1043	0.2378	0.0972	0.3598	-11.5401	-17.8303	-10.1124
15	1.4216	0.1597	0.8691	1.3505	-0.2599	1.7605	-0.2684	-0.0762	0.4718	-0.2756	0.0195	0.1603	-0.4461	-0.1904	0.1985	0.3873	0.0856	-0.0787	0.1889	-0.0261	0.3277	-15.1619	-18.1565	6.2341
16	0.9465	1.5671	0.0983	5.8629	0.0424	4.568	-0.0047	-0.0637	0.0136	0.0713	-0.0808	-0.0347	-0.0197	0.0033	0.1142	0.0893	0.0435	0.0268	0.1873	-0.002	0.1643	-8.5307	-36.715	20.102

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 51 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 52 through 91 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 92 through 149 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 150 through 252 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 253 through 301 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 302 through 347 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 348 through 466 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 467 through 505 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 506 through 560 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 20 through 51 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 52 through 149 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 150 through 282 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 283 through 320 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 321 through 404 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 405 through 531 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 532 through 561 )

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