PDB-4pe6: Crystal structure of ABC transporter solute binding protein from ...

ID or keywords:

Entry

Database: PDB / ID: 4pe6

Title

Crystal structure of ABC transporter solute binding protein from Thermobispora bispora DSM 43833

Components

Putative ABC transporter

Keywords

SOLUTE-BINDING PROTEIN / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / ABC transporter / solute binding protein

Function / homology

Periplasmic binding protein / Periplasmic binding protein domain / Periplasmic binding protein-like I / (2R,3S)-2,3,4-trihydroxybutanoic acid / Putative ABC transporter

Function and homology information

Biological species

Thermobispora bispora (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.86 Å

Authors

Chang, C. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: to be published
Title: Crystal structure of ABC transporter solute binding protein from Thermobispora bispora DSM 43833
Authors: Chang, C. / Li, H. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Apr 22, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 7, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 4, 2015	Group: Derived calculations
Revision 1.2	Nov 22, 2017	Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3	Dec 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4pe6.cif.gz	258.6 KB	Display	PDBx/mmCIF format
PDB format	pdb4pe6.ent.gz	210.5 KB	Display	PDB format
PDBx/mmJSON format	4pe6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4pe6_validation.pdf.gz	441.3 KB	Display	wwPDB validaton report
Full document	4pe6_full_validation.pdf.gz	441.4 KB	Display
Data in XML	4pe6_validation.xml.gz	26.6 KB	Display
Data in CIF	4pe6_validation.cif.gz	38.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pe/4pe6 ftp://data.pdbj.org/pub/pdb/validation_reports/pe/4pe6	HTTPS FTP

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Related structure data

Similar structure data	6ncg-2 4rpf-2 5uv4-d 6x5g-d 5z94-1 6xbx-1 6jbc-d 4zji-3 4f8j-d 6d71-d 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: MCSG-APC111251

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative ABC transporter

B: Putative ABC transporter

hetero molecules

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

1

A: Putative ABC transporter

hetero molecules

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

2

B: Putative ABC transporter

hetero molecules

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

Unit cell

Length a, b, c (Å)	52.724, 77.375, 79.472
Angle α, β, γ (deg.)	90.000, 90.370, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Putative ABC transporter Mass: 36259.203 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobispora bispora (bacteria) / Strain: DSM 43833 / Gene: Tbis_1193 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D6Y8L8
#2: Chemical	ChemComp-LTH / (2R,3S)-2,3,4-trihydroxybutanoic acid / L-Threonic acid Mass: 136.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₈O₅
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.27 Å³/Da / Density % sol: 45.74 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M MES, 30% PEG4000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97915 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2013

Radiation

Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97915 Å / Relative weight: 1

Reflection

Resolution: 1.86→50 Å / Num. obs: 53201 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.088 / Χ²: 0.883 / Net I/av σ(I): 13.698 / Net I/σ(I): 10.8 / Num. measured all: 193114

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	% possible all
1.86-1.89	2.8	0.416	2492	0.926	94
1.89-1.93	3.1	0.392	2614	0.929	99.1
1.93-1.96	3.5	0.337	2640	0.911	99.8
1.96-2	3.6	0.32	2683	0.905	100
2-2.05	3.7	0.271	2660	0.922	100
2.05-2.09	3.7	0.229	2685	0.963	100
2.09-2.15	3.7	0.201	2653	0.914	100
2.15-2.21	3.7	0.18	2662	0.94	100
2.21-2.27	3.7	0.155	2674	0.962	100
2.27-2.34	3.7	0.141	2624	0.887	100
2.34-2.43	3.8	0.123	2672	0.849	100
2.43-2.52	3.8	0.111	2687	0.847	100
2.52-2.64	3.8	0.101	2676	0.825	100
2.64-2.78	3.8	0.089	2664	0.834	100
2.78-2.95	3.8	0.082	2656	0.821	100
2.95-3.18	3.7	0.078	2680	0.818	100
3.18-3.5	3.7	0.078	2697	0.896	99.9
3.5-4.01	3.7	0.077	2681	0.928	99.9
4.01-5.05	3.6	0.068	2696	0.805	99.9
5.05-50	3.6	0.071	2705	0.797	98

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
REFMAC	5.7.0029	refinement
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 1.86→31.66 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.935 / SU B: 5.645 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2176	2463	5.1 %	RANDOM
R_work	0.1823	46282	-	-
obs	0.1841	48745	91.01 %	-

Solvent computation

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

Displacement parameters

B_iso max: 116.61 Å² / B_iso mean: 27.637 Å² / B_iso min: 13.63 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.34 Å²	0 Å²	0.18 Å²
2-	-	2.34 Å²	-0 Å²
3-	-	-	-1 Å²

Refinement step

Cycle: final / Resolution: 1.86→31.66 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4835	0	18	340	5193
B_iso mean	-	-	18.72	30.83	-
Num. residues	-	-	-	-	646

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.02	4985
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4819
X-RAY DIFFRACTION	r_angle_refined_deg	1.293	1.973	6810
X-RAY DIFFRACTION	r_angle_other_deg	0.783	3.002	11118
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.54	5	650
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	40.654	25.957	188
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.956	15	762
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.102	15	14
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	788
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	5690
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1020

LS refinement shell

Resolution: 1.86→1.911 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.268	98	-
R_work	0.231	2147	-
all	-	2245	-
obs	-	-	56.82 %

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	2.3281	-0.0287	-1.4598	0.37	0.2217	2.7563	-0.0687	-0.0247	-0.2418	0.0338	-0.0238	0.0446	0.2693	-0.1202	0.0925	0.2018	-0.0355	0.0021	0.0273	0.0154	0.1601	33.1876	30.127	80.881
2	3.3604	0.045	-0.2426	0.5731	-0.5127	0.9839	0.0102	0.3854	-0.0525	-0.0533	-0.0248	0.0377	0.0424	-0.3219	0.0146	0.1596	-0.0095	-0.0264	0.2465	-0.0378	0.1198	26.5766	37.2834	69.9755
3	2.3895	-0.3184	-0.738	0.0793	0.2828	1.2956	0.0953	0.012	0.227	-0.0052	-0.0045	-0.0429	-0.0516	-0.1137	-0.0909	0.1765	0.0143	0.0013	0.0544	-0.011	0.1835	34.9017	45.0059	76.6803
4	2.03	-0.3713	-0.9542	0.4728	-0.0024	0.9363	0.0285	0.0712	0.2146	-0.0013	0.0498	-0.0295	-0.0186	0.0578	-0.0783	0.1658	-0.0041	-0.0157	0.0571	-0.0201	0.1604	56.9512	41.9357	63.5693
5	1.784	-0.8077	-0.2492	1.0967	0.8561	0.8316	-0.0471	0.1399	-0.2013	0.0138	0.0314	0.0008	-0.0069	0.0546	0.0157	0.2016	0.0193	0.0058	0.0474	-0.0569	0.1853	58.4667	29.7876	58.4273
6	9.0679	-0.2348	-3.1365	8.8731	-3.1465	2.2636	-0.3088	-0.4887	-0.8563	-0.2944	-0.3424	-0.8369	0.2296	0.3068	0.6512	0.2458	0.0994	0.0761	0.0635	0.0939	0.3766	59.2805	23.1066	71.8398
7	2.0294	-0.6614	-1.4186	0.3409	0.304	1.2352	-0.0471	-0.2605	0.0038	0.051	0.0613	-0.0203	0.0575	0.1948	-0.0142	0.1929	0.0105	-0.0246	0.0909	-0.0147	0.1508	44.1538	38.7554	83.4158
8	2.979	-1.9017	-2.5015	2.0823	1.6358	2.1173	-0.3192	-0.5119	-0.2281	0.27	0.11	-0.0585	0.2914	0.4044	0.2092	0.2149	0.0729	-0.0287	0.1828	0.0599	0.152	49.7574	29.7189	84.9308
9	1.6674	-2.8248	1.1001	7.526	3.2013	10.1398	0.0465	0.0123	0.0146	-0.1052	0.1927	-0.0968	-0.001	0.5465	-0.2392	0.1979	-0.0764	-0.0282	0.3607	-0.2641	0.2381	47.1315	46.9429	92.779
10	6.9109	-7.6088	-9.6058	8.4819	10.8287	13.9685	-0.3858	-0.0738	-0.2309	0.3262	-0.2402	0.3743	0.2873	-0.6504	0.626	0.2527	0.2265	-0.0559	0.9956	-0.3427	0.2883	51.8369	30.7585	89.2179
11	3.2748	0.3716	2.0401	0.1854	0.5638	2.0773	-0.0336	0.0064	0.1853	-0.0387	-0.0351	0.0126	-0.1737	-0.0878	0.0687	0.2064	0.0197	-0.0192	0.024	-0.0007	0.165	8.8622	16.6592	42.988
12	2.0222	0.6319	0.1612	0.5628	-0.0327	2.7722	-0.0352	-0.2061	0.2483	-0.0088	-0.091	0.1214	-0.2654	-0.3864	0.1262	0.1515	0.0627	-0.0176	0.0871	-0.0165	0.139	2.2433	15.7678	42.0082
13	1.7535	-0.0433	0.3894	0.0362	0.0395	1.0019	0.1119	-0.0072	-0.2379	-0.0306	0.0339	-0.0185	0.0734	-0.0942	-0.1458	0.1878	-0.0239	-0.0318	0.0561	-0.0194	0.1818	8.6861	3.8038	42.4837
14	2.2226	0.1239	1.1178	0.7078	0.2961	0.7909	0.0732	-0.0679	-0.1098	0.024	0.0355	-0.0408	0.0016	0.0483	-0.1088	0.1656	-0.0091	-0.0097	0.0432	-0.0148	0.1525	30.1522	8.2092	56.5845
15	1.9338	0.3583	-0.3426	1.4239	1.1292	1.1122	-0.0664	-0.1019	0.1678	-0.0219	0.1366	-0.0396	0.0039	0.1547	-0.0701	0.1841	-0.0294	-0.0275	0.0506	-0.0382	0.1842	33.3606	18.7571	60.2592
16	9.8346	2.5621	2.783	7.6834	-3.5781	3.4323	-0.0666	0.1896	0.5589	0.3335	-0.4415	-0.3879	-0.2687	0.3617	0.5081	0.3293	-0.0949	-0.0746	0.0539	0.0483	0.2632	32.7918	25.8608	47.7102
17	2.3188	0.8857	1.9682	0.3651	0.7378	2.3083	-0.0557	0.1252	0.0768	-0.0702	0.05	-0.0032	-0.1928	0.0455	0.0057	0.2071	-0.0097	0.0034	0.0642	-0.0089	0.1617	16.3959	12.2743	36.0358
18	1.9728	0.8373	1.7392	1.2496	1.0083	1.6224	-0.1	0.5014	0.025	-0.0951	0.1057	-0.0553	-0.1111	0.4002	-0.0057	0.1781	-0.0383	0.0222	0.1568	0.016	0.1183	22.2588	14.2325	34.1117
19	3.4561	-1.3196	-6.5984	4.2065	1.8876	12.7772	-0.14	-0.5212	-0.0964	-0.4993	-0.0514	-0.3583	0.2442	1.1588	0.1914	0.257	-0.0429	0.0582	0.4259	-0.1727	0.2131	23.9415	3.9459	27.0441
20	1.4053	-5.4172	-0.3389	27.2346	-5.6817	7.8611	0.4735	0.6231	-0.6036	-1.4431	-1.594	1.5013	-0.723	-0.8748	1.1204	0.6118	-0.0916	-0.3869	0.6705	-0.2563	0.4141	24.2292	22.8384	31.5453

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	47 - 86
2	X-RAY DIFFRACTION	2	A	87 - 110
3	X-RAY DIFFRACTION	3	A	111 - 162
4	X-RAY DIFFRACTION	4	A	163 - 222
5	X-RAY DIFFRACTION	5	A	223 - 264
6	X-RAY DIFFRACTION	6	A	265 - 279
7	X-RAY DIFFRACTION	7	A	280 - 321
8	X-RAY DIFFRACTION	8	A	322 - 350
9	X-RAY DIFFRACTION	9	A	351 - 360
10	X-RAY DIFFRACTION	10	A	361 - 368
11	X-RAY DIFFRACTION	11	B	47 - 67
12	X-RAY DIFFRACTION	12	B	68 - 110
13	X-RAY DIFFRACTION	13	B	111 - 162
14	X-RAY DIFFRACTION	14	B	163 - 228
15	X-RAY DIFFRACTION	15	B	229 - 264
16	X-RAY DIFFRACTION	16	B	265 - 279
17	X-RAY DIFFRACTION	17	B	280 - 307
18	X-RAY DIFFRACTION	18	B	308 - 354
19	X-RAY DIFFRACTION	19	B	355 - 362
20	X-RAY DIFFRACTION	20	B	363 - 370

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