PDB-5wnn: Crystal structure of Phosphate-binding protein PstS protein from ...

ID or keywords:

Entry

Database: PDB / ID: 5wnn

Title

Crystal structure of Phosphate-binding protein PstS protein from Burkholderia pseudomallei

Components

Phosphate-binding protein PstS

Keywords

PHOSPHATE BINDING PROTEIN / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Burkholderia pseudomallei

Function / homology

Function and homology information

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

Biological species

Burkholderia pseudomallei (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal structure of Phosphate-binding protein PstS protein from Burkholderia pseudomallei
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Aug 1, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 30, 2017	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	5wnn.cif.gz	266.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5wnn.ent.gz	211.9 KB	Display	PDB format
PDBx/mmJSON format	5wnn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	5wnn_validation.pdf.gz	444.2 KB	Display	wwPDB validaton report
Full document	5wnn_full_validation.pdf.gz	444.3 KB	Display
Data in XML	5wnn_validation.xml.gz	29.1 KB	Display
Data in CIF	5wnn_validation.cif.gz	44.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wn/5wnn ftp://data.pdbj.org/pub/pdb/validation_reports/wn/5wnn	HTTPS FTP

-
Related structure data

Related structure data	1ixhS S: Starting model for refinement
Similar structure data	2z22-2 1a54-d 1ixg-d 5ub4-1 2zgt-d 1qui-d 1quj-d 5v40-1 1pc3-2 4lvq-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
Other databases	TargetTrack: BupsE.18050.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Phosphate-binding protein PstS

B: Phosphate-binding protein PstS

hetero molecules

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

1

A: Phosphate-binding protein PstS

hetero molecules

defined by author
Evidence: gel filtration
38.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Phosphate-binding protein PstS

hetero molecules

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

Unit cell

Length a, b, c (Å)	116.640, 59.840, 101.090
Angle α, β, γ (deg.)	90.000, 120.970, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-401- K
2	1	B-401- K
3	1	A-581- HOH
4	1	A-744- HOH
5	1	A-807- HOH
6	1	B-534- HOH

#1: Protein	Phosphate-binding protein PstS Mass: 38484.562 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria) Strain: K96243 / Gene: pstS, BPSL1359 / Plasmid: BupsE.18050.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q63V82
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 599 / 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: 1.97 Å³/Da / Density % sol: 37.41 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Optimization screen around Rigaku Reagents JCSG+ screen, G9: 30% PEG2000 MME, 100 mM potassium thiocyanate, 20 mg/mL BupsE.18050.a.A1.PS01695, cryoprotectant: 20% ethylene glycol, tray 251795e1, puck cul4-7

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU FR / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 19, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.85→43.339 Å / Num. obs: 49982 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 2.648 % / B_iso Wilson estimate: 23.69 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.041 / R_rim(I) all: 0.05 / Χ²: 1.031 / Net I/σ(I): 15.23

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	1.712	0.388	2.03	3396	0.863	0.549	90.3
1.9-1.95	1.74	0.262	2.72	3433	0.918	0.371	92.8
1.95-2.01	1.768	0.215	3.53	3375	0.917	0.305	94.7
2.01-2.07	1.794	0.161	4.84	3365	0.953	0.228	96.6
2.07-2.14	1.953	0.137	6.05	3312	0.966	0.19	98.1
2.14-2.21	2.29	0.113	7.97	3202	0.976	0.151	98.5
2.21-2.29	2.417	0.094	9.52	3105	0.987	0.123	98.8
2.29-2.39	2.504	0.082	10.97	2992	0.989	0.106	98.9
2.39-2.49	2.638	0.071	12.44	2895	0.992	0.091	98.9
2.49-2.62	2.795	0.063	14.51	2759	0.994	0.08	99
2.62-2.76	3.048	0.059	16.17	2602	0.995	0.072	99.3
2.76-2.93	3.551	0.055	20.17	2503	0.997	0.065	99.6
2.93-3.13	3.693	0.052	23.09	2340	0.997	0.061	99
3.13-3.38	3.678	0.04	28.13	2183	0.998	0.047	99.2
3.38-3.7	3.634	0.033	34.33	2024	0.998	0.038	99.2
3.7-4.14	3.632	0.03	37.88	1832	0.998	0.035	99.2
4.14-4.78	3.632	0.028	39.9	1603	0.998	0.032	98.6
4.78-5.85	3.692	0.027	39.62	1382	0.999	0.032	99.6
5.85-8.27	3.663	0.027	39.03	1086	0.999	0.032	98.7
8.27-43.339	3.427	0.027	41.63	593	0.999	0.032	96.4

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2 Å	43.34 Å
Translation	2 Å	43.34 Å

-
Processing

Software

Name	Classification
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1IXH

1ixh

Resolution: 1.85→43.339 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.7

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2175	1814	3.63 %	0
R_work	0.1702	-	-	-
obs	0.1719	49948	97.55 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 79.66 Å² / B_iso mean: 30.092 Å² / B_iso min: 10.29 Å²

Refinement step

Cycle: final / Resolution: 1.85→43.339 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4684	0	12	610	5306
B_iso mean	-	-	16.34	35.65	-
Num. residues	-	-	-	-	640

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4852
X-RAY DIFFRACTION	f_angle_d	0.775	6650
X-RAY DIFFRACTION	f_chiral_restr	0.053	749
X-RAY DIFFRACTION	f_plane_restr	0.005	861
X-RAY DIFFRACTION	f_dihedral_angle_d	12.775	2790

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 13

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8501-1.9001	0.3009	155	0.24	3383	3538	91
1.9001-1.956	0.3017	169	0.2359	3476	3645	93
1.956-2.0191	0.3058	135	0.2266	3587	3722	95
2.0191-2.0913	0.2746	144	0.2059	3658	3802	97
2.0913-2.175	0.2636	139	0.2009	3721	3860	99
2.175-2.274	0.2579	142	0.1938	3737	3879	99
2.274-2.3939	0.2202	138	0.1806	3749	3887	99
2.3939-2.5438	0.2479	128	0.1829	3761	3889	99
2.5438-2.7402	0.2424	126	0.1793	3793	3919	99
2.7402-3.0159	0.2283	132	0.1783	3777	3909	100
3.0159-3.4522	0.2318	132	0.1584	3810	3942	99
3.4522-4.3487	0.1662	143	0.1426	3807	3950	99
4.3487-43.351	0.1575	131	0.1412	3875	4006	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	0.9979	-0.2705	1.2401	1.8505	-1.8163	4.0321	-0.2643	-0.2648	0.0687	0.4404	-0.0206	0.4308	-0.3302	-1.4379	0.1871	0.3339	0.0128	0.1306	0.5104	-0.1208	0.44	-11.9293	8.9311	43.3828
2	2.798	-0.6365	1.9379	2.8391	0.4618	1.6596	-0.1015	-0.0165	-0.4427	0.6972	0.2079	0.5743	0.3608	-0.8639	-0.0871	0.5117	-0.1653	0.2208	0.6352	0.0508	0.5164	-13.8836	-3.052	51.2635
3	3.9513	0.8101	-0.1615	2.6552	0.0817	3.236	-0.0753	0.6155	0.2962	-0.3885	0.124	-0.0168	-0.5176	-0.3643	-0.0571	0.273	0.0423	-0.0037	0.2582	0.0503	0.1994	-21.1236	-20.3408	-0.438
4	2.5562	-0.0306	0.213	2.3594	0.8251	3.8976	-0.0484	0.3818	-0.5376	-0.0554	0.0047	0.1322	0.5927	-0.5302	0.0125	0.2357	-0.0527	0.0103	0.2394	-0.0739	0.2765	-23.0047	-35.6153	0.5541
5	2.104	0.0788	-1.2967	0.5085	0.4255	2.6415	0.0165	-0.1917	0.0054	0.0298	0.044	-0.0129	-0.0129	-0.0296	-0.059	0.144	0.0394	-0.0163	0.1725	0.0326	0.1492	-27.3584	-24.1002	24.4685
6	0.8529	-1.0851	-0.7649	5.6334	4.4479	6.6471	-0.177	-0.3335	-0.4171	-0.0988	0.3477	-0.5798	0.5331	1.1011	-0.209	0.2685	0.0962	0.0471	0.4977	0.0704	0.3545	-9.7468	-30.8465	15.3361
7	2.0464	-0.3588	-0.6736	1.3433	0.9088	4.8577	-0.0452	0.0568	0.0197	-0.1157	0.0584	-0.049	-0.131	0.1625	-0.0066	0.109	0.0095	-0.0153	0.1146	0.0022	0.1746	-13.3532	-25.8116	5.8069
8	4.0383	2.2096	5.0744	3.5549	4.6181	9.3502	0.0449	0.1766	-0.2758	-0.2156	-0.0091	-0.045	0.0618	0.2241	-0.0192	0.1763	0.0042	0.0296	0.1937	-0.0565	0.2214	-8.0084	-33.5376	-4.2175
9	3.8028	-1.0562	-0.327	1.493	-0.7701	4.2244	-0.2252	-0.2607	0.6039	0.701	-0.083	0.1593	-0.3436	-0.4594	0.2569	0.3776	-0.0157	0.0632	0.2197	-0.107	0.3714	-3.9884	11.895	43.4638
10	4.4043	-2.0918	-1.2143	3.2556	1.4608	3.7898	-0.169	-0.413	0.1862	0.6366	0.0311	0.1118	-0.1323	0.0306	0.1306	0.403	-0.067	0.0462	0.1984	-0.0378	0.2715	2.4051	6.198	45.6767
11	1.8191	-0.1261	-0.0804	0.9182	0.4534	1.2151	-0.0485	0.022	-0.2565	0.2076	-0.0441	0.2143	0.4096	-0.2664	0.0621	0.26	-0.0681	0.0331	0.1843	-0.0453	0.2753	-0.6469	0.9192	30.4682
12	3.336	0.4089	1.7666	1.7034	-0.3971	5.4969	-0.0081	0.7007	0.1323	-0.1922	-0.1771	0.0936	0.2724	0.2969	0.1869	0.1996	0.0143	-0.0308	0.353	-0.0041	0.1546	6.2315	5.6953	6.7452
13	2.2078	0.5929	0.9756	1.3583	-0.4636	0.8999	-0.0084	0.3192	-0.376	0.1312	-0.1601	0.1324	0.7596	-0.0007	0.0959	0.3549	-0.046	0.0358	0.2052	-0.088	0.2456	5.3594	-4.3204	23.8071
14	2.7365	-1.1272	-1.1889	1.8749	0.0556	4.8837	0.0197	0.1155	0.2188	0.1106	-0.1102	0.0998	-0.2609	0.057	0.0876	0.1459	-0.0381	-0.0257	0.1672	0.0174	0.1962	5.6719	11.4354	24.8724
15	5.4138	1.5861	2.5468	2.5437	-0.843	2.4106	-0.0464	0.4286	0.0185	-0.1951	-0.0184	0.5179	0.1657	-0.6475	0.1148	0.1901	-0.0721	-0.0309	0.4949	-0.0418	0.2901	-6.7764	7.5136	16.3413
16	1.5064	0.9862	-0.5677	0.9785	-0.0119	0.622	-0.0018	0.0836	-0.7122	0.1857	-0.0025	0.5503	0.4468	-0.7908	-0.0105	0.3648	-0.2418	0.1114	0.6055	-0.1554	0.6476	-13.298	-2.5101	30.3522
17	0.4636	-0.0589	-0.2389	2.4985	-0.3121	0.1593	-0.2258	0.0945	-0.288	0.3153	0.1037	0.4505	0.2937	-0.3685	-0.0706	0.2138	-0.3182	0.123	0.3713	-0.1496	0.3887	-6.8915	-1.4802	34.569

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 287 through 317 )	B	287 - 317
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 318 through 341 )	B	318 - 341
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 22 through 66 )	A	22 - 66
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 67 through 88 )	A	67 - 88
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 89 through 240 )	A	89 - 240
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 241 through 258 )	A	241 - 258
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 259 through 317 )	A	259 - 317
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 318 through 341 )	A	318 - 341
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 22 through 45 )	B	22 - 45
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 46 through 66 )	B	46 - 66
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 67 through 124 )	B	67 - 124
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 125 through 152 )	B	125 - 152
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 153 through 191 )	B	153 - 191
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 192 through 221 )	B	192 - 221
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 222 through 240 )	B	222 - 240
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 241 through 260 )	B	241 - 260
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 261 through 286 )	B	261 - 286

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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