PDB-4n01: The crystal structure of a periplasmic binding protein from Veill...

ID or keywords:

Entry

Database: PDB / ID: 4n01

Title

The crystal structure of a periplasmic binding protein from Veillonella parvula dsm 2008

Components

Periplasmic binding protein

Keywords

TRANSPORT PROTEIN / STRUCTURAL GENOMICS / PSI-BIOLOGY / PROTEIN STRUCTURE INITIATIVE / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG / ALPHA/BETA FOLD / SOLUTE BINDING PROTEIN / PERIPLASMIC

Function / homology

ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / FORMIC ACID / Periplasmic binding protein

Function and homology information

Biological species

Veillonella parvula (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.797 Å

Authors

Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: The crystal structure of a periplasmic binding protein from Veillonella parvula dsm 2008
Authors: Wu, R. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

History

Deposition	Sep 30, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4n01.cif.gz	263.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4n01.ent.gz	214.5 KB	Display	PDB format
PDBx/mmJSON format	4n01.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/n0/4n01 ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n01	HTTPS FTP

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Related structure data

Similar structure data	1bgu-d 1aoa-d 1wly-d 1nhc-2 6xhk-d 4x3f-2 5hgr-1 3mg3-3 5teu-2 3mg1-2 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 - HomologyF&H Search
Other databases	TargetTrack: MCSG-APC100847

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Periplasmic binding protein

B: Periplasmic binding protein

hetero molecules

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

1

A: Periplasmic binding protein

hetero molecules

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

2

B: Periplasmic binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	107.192, 46.330, 108.550
Angle α, β, γ (deg.)	90.00, 119.62, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Periplasmic binding protein Mass: 38018.570 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 29-334 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Veillonella parvula (bacteria) / Strain: DSM 2008 / Gene: Vpar_1351 / Plasmid: PMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MAGIC / References: UniProt: D1BNS2
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.08 Å³/Da / Density % sol: 60.09 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.6 Details: 0.2 M Ammonium Formate pH 6.6, 20% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9789666 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 21, 2013 / Details: mirrors
Radiation	Monochromator: Si 111, channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9789666 Å / Relative weight: 1
Reflection	Resolution: 1.8→50 Å / Num. all: 86319 / Num. obs: 82694 / % possible obs: 99.6 % / Redundancy: 3.6 % / R_sym value: 0.091 / Net I/σ(I): 8.1
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.19 / R_sym value: 0.492 / % possible all: 99

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Processing

Software

Name	Version	Classification
HKL-3000		data collection
MLPHARE		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.797→28.141 Å / SU ML: 0.18 / σ(F): 1.39 / Phase error: 20.35 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.2045	3787	4.98 %
R_work	0.1711	-	-
obs	0.1728	75979	87.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.797→28.141 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4664	0	41	488	5193

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	4990
X-RAY DIFFRACTION	f_angle_d	0.982	6776
X-RAY DIFFRACTION	f_dihedral_angle_d	13.603	1877
X-RAY DIFFRACTION	f_chiral_restr	0.071	745
X-RAY DIFFRACTION	f_plane_restr	0.005	878

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 (%)
1.7965-1.8193	0.3017	60	0.2345	1072	X-RAY DIFFRACTION	36
1.8193-1.8432	0.2782	86	0.2232	1635	X-RAY DIFFRACTION	53
1.8432-1.8684	0.2529	96	0.2049	1718	X-RAY DIFFRACTION	57
1.8684-1.8951	0.266	101	0.2068	1861	X-RAY DIFFRACTION	62
1.8951-1.9234	0.2329	105	0.2035	2043	X-RAY DIFFRACTION	66
1.9234-1.9535	0.2533	92	0.1962	2122	X-RAY DIFFRACTION	70
1.9535-1.9855	0.2382	134	0.1941	2293	X-RAY DIFFRACTION	76
1.9855-2.0197	0.2634	121	0.1875	2472	X-RAY DIFFRACTION	81
2.0197-2.0564	0.2009	142	0.1911	2550	X-RAY DIFFRACTION	85
2.0564-2.096	0.2176	147	0.1936	2793	X-RAY DIFFRACTION	91
2.096-2.1387	0.2235	151	0.1895	2805	X-RAY DIFFRACTION	93
2.1387-2.1852	0.2157	137	0.1881	2979	X-RAY DIFFRACTION	96
2.1852-2.236	0.2213	165	0.1809	2968	X-RAY DIFFRACTION	98
2.236-2.2919	0.2419	142	0.1841	3009	X-RAY DIFFRACTION	99
2.2919-2.3539	0.2058	174	0.1784	3008	X-RAY DIFFRACTION	99
2.3539-2.4231	0.2358	164	0.1765	3090	X-RAY DIFFRACTION	100
2.4231-2.5013	0.2308	183	0.183	3001	X-RAY DIFFRACTION	100
2.5013-2.5906	0.2131	163	0.1736	3055	X-RAY DIFFRACTION	100
2.5906-2.6942	0.2094	176	0.1761	3034	X-RAY DIFFRACTION	100
2.6942-2.8168	0.2308	151	0.1745	3072	X-RAY DIFFRACTION	100
2.8168-2.9651	0.2196	147	0.1786	3076	X-RAY DIFFRACTION	100
2.9651-3.1506	0.1911	169	0.1759	3083	X-RAY DIFFRACTION	100
3.1506-3.3935	0.1836	146	0.17	3097	X-RAY DIFFRACTION	100
3.3935-3.7343	0.1929	171	0.1604	3048	X-RAY DIFFRACTION	100
3.7343-4.2731	0.1695	165	0.1445	3095	X-RAY DIFFRACTION	99
4.2731-5.3775	0.1537	150	0.1339	3122	X-RAY DIFFRACTION	99
5.3775-28.1447	0.1952	149	0.169	3091	X-RAY DIFFRACTION	95

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	5.8257	0.4416	-4.325	6.3667	-1.0814	3.3643	0.064	0.2655	-0.3044	-0.4813	-0.011	-0.268	0.2449	0.069	-0.0298	0.2467	0.0175	-0.1466	0.1834	-0.0054	0.2259	27.3539	6.8819	30.7475
2	1.0257	-0.6072	0.1787	1.4486	-1.4761	1.7861	0.1403	-0.0649	0.0829	0.1059	-0.1004	-0.1522	-0.0863	0.1874	0.009	0.2326	-0.0196	-0.1344	0.1805	-0.0174	0.219	23.5481	24.6248	38.3254
3	1.3982	-0.4781	0.427	2.7477	0.0914	1.7574	0.0673	0.0616	0.0602	-0.1331	-0.1785	-0.649	-0.0343	0.4705	0.0311	0.172	-0.0301	-0.1307	0.2506	0.0498	0.2984	32.5869	22.5016	35.2662
4	1.9577	-0.3402	0.5422	1.4983	-0.6147	2.8819	0.0573	-0.0124	-0.0735	0.0773	-0.0719	-0.0792	0.1609	0.0612	-0.0359	0.1493	0.0019	-0.0694	0.1085	-0.0037	0.1573	17.9507	15.1227	31.3906
5	6.9466	-4.2513	5.4546	6.0345	-5.4109	6.8812	-0.0469	-0.0783	-0.1576	0.282	0.2152	0.3787	-0.1568	-0.1798	-0.1069	0.0949	-0.0334	0.0117	0.0864	-0.0098	0.1422	3.0589	22.2741	33.9552
6	0.6512	-0.5525	-0.7629	3.0461	-0.7097	3.8663	0.0397	0.0251	-0.0074	-0.1609	-0.1259	-0.1827	0.0452	0.2659	0.0727	0.1181	0.0027	-0.0544	0.1217	-0.0011	0.1167	13.4663	29.1746	11.1793
7	1.272	0.0145	-1.0089	1.959	-0.8374	1.8826	0.0718	0.0148	0.1803	0.2038	0.0076	-0.1081	-0.3499	0.1094	-0.0929	0.1459	-0.0277	-0.0402	0.1171	-0.0145	0.1644	14.5274	40.5224	16.7046
8	5.1448	-1.3901	4.8789	8.7083	-3.7245	8.3862	-0.1363	-0.4326	0.3985	0.4771	0.1187	0.4223	-0.606	-0.2982	0.058	0.1352	-0.0129	0.0102	0.1299	-0.0211	0.1925	2.8597	34.2973	24.9721
9	9.2795	0.5285	4.9794	5.0256	0.6736	9.451	0.0088	0.3487	0.4171	-0.3641	0.0673	0.0658	-0.3473	-0.1752	-0.0553	0.2329	0.053	0.1378	0.1422	0.0481	0.2083	-27.3224	28.9693	30.6613
10	0.8991	-0.4923	-0.692	0.4766	0.424	2.1547	0.1252	-0.0017	0.0161	0.1553	-0.0993	0.2129	0.0539	-0.2859	0.5153	0.2835	0.0008	0.2105	0.2007	-0.0074	0.2425	-26.3966	16.4725	39.0521
11	6.3789	1.059	0.5103	1.7551	0.108	2.6742	0.149	-0.0407	-0.1324	0.1181	-0.1392	0.0565	0.05	-0.0429	0.0017	0.2556	0.0114	0.1352	0.1356	0.0367	0.2033	-22.1984	8.9935	38.1066
12	5.1336	-2.2866	1.0798	2.4138	-1.0696	3.0312	-0.1196	-0.2152	-0.3901	0.1885	-0.0702	0.3867	0.1681	-0.2818	0.0553	0.2408	-0.0478	0.1541	0.1598	-0.0139	0.2348	-27.6999	5.2722	38.7494
13	4.4404	-0.7137	-1.3537	1.8668	0.4331	5.0334	-0.0968	0.2464	-0.135	0.0054	-0.2083	0.6289	0.1156	-0.574	0.2017	0.2489	-0.015	0.1483	0.2308	-0.0655	0.3153	-34.3883	16.3751	33.2607
14	6.5082	-2.9369	-2.6694	2.3361	2.2605	4.4174	0.0601	0.1013	0.1635	0.0912	-0.0762	0.3348	-0.1517	-0.4061	-0.0486	0.213	0.0236	0.0979	0.1486	0.007	0.2295	-26.6909	21.8132	29.1641
15	3.9775	-2.0595	-4.238	1.4608	2.4704	6.1974	-0.0279	-0.0635	-0.0112	0.1908	-0.0619	0.2324	0.1142	0.0003	0.1094	0.1787	-0.019	0.0613	0.1188	0.0124	0.186	-14.2765	20.5244	34.553
16	5.6971	-3.3869	-4.5895	5.7708	4.9921	6.7261	0.1295	-0.2323	0.1793	0.2173	0.2022	-0.2839	-0.0234	0.2395	-0.273	0.1139	-0.036	-0.0175	0.1173	0.0105	0.1793	-2.9949	13.4281	33.5059
17	1.2383	-0.6126	0.7904	3.3284	0.7286	3.9961	0.0301	0.009	0.0366	-0.1477	-0.0893	0.1681	-0.1113	-0.1838	0.0586	0.105	-0.0029	0.0408	0.1112	0.0059	0.0941	-13.1745	6.8828	11.3538
18	3.5545	0.356	-0.7094	2.9593	-0.4995	6.7938	0.0358	-0.2621	-0.2438	0.503	0.0454	0.3518	0.4412	-0.3536	-0.0408	0.1742	-0.0112	0.0601	0.128	0.0118	0.2085	-16.4558	-6.8207	18.6219
19	1.2913	0.9496	1.2101	3.1415	1.0021	1.1438	0.0617	0.0889	-0.0941	0.1074	0.0502	-0.0803	0.189	0.0425	-0.0676	0.0922	-0.0118	0.013	0.0994	0.0184	0.1006	-12.7321	-2.6494	15.0794
20	6.7064	-3.2202	-5.3309	3.9282	4.0835	8.6274	-0.1384	-0.2547	-0.4385	0.4306	0.0832	-0.3779	0.5276	0.3008	0.0612	0.1766	-0.0195	-0.0028	0.1405	0.0265	0.2373	-3.1621	1.7723	25.4139

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 40 through 56 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 57 through 94 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 95 through 145 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 146 through 178 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 179 through 200 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 201 through 259 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 260 through 316 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 317 through 333 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 40 through 56 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 57 through 71 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 72 through 94 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 95 through 113 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 114 through 138 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 139 through 161 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 162 through 178 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 179 through 200 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 201 through 259 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 260 through 287 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 288 through 316 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 317 through 333 )

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