PDB-4exl: Crystal structure of phosphate ABC transporter, periplasmic phosp...

ID or keywords:

Entry

Database: PDB / ID: 4exl

Title

Crystal structure of phosphate ABC transporter, periplasmic phosphate-binding protein PstS 1 (PBP1) from Streptococcus pneumoniae Canada MDR_19A

Components

Phosphate-binding protein pstS 1

Keywords

TRANSPORT PROTEIN / Center for Structural Genomics of Infectious Diseases (CSGID) / NIAID / National Institute of Allergy and Infectious Diseases / alpha and beta protein / Periplasmic binding protein-like II fold / phosphate ABC transporter / extracellular

Function / homology

Function and homology information

phosphate ion transport / phosphate ion binding / plasma membrane
Similarity search - Function

Biological species

Streptococcus pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal structure of phosphate ABC transporter, periplasmic phosphate-binding protein PstS 1 (PBP1) from Streptococcus pneumoniae Canada MDR_19A
Authors: Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Minasov, G. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Apr 30, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 30, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jul 3, 2013	Group: Database references / Structure summary
Revision 1.2	Sep 13, 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 / 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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4exl.cif.gz	430.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4exl.ent.gz	354.3 KB	Display	PDB format
PDBx/mmJSON format	4exl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4exl_validation.pdf.gz	452.2 KB	Display	wwPDB validaton report
Full document	4exl_full_validation.pdf.gz	460.3 KB	Display
Data in XML	4exl_validation.xml.gz	52.4 KB	Display
Data in CIF	4exl_validation.cif.gz	80.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/4exl ftp://data.pdbj.org/pub/pdb/validation_reports/ex/4exl	HTTPS FTP

-
Related structure data

Related structure data	1twyS 4lat S: Starting model for refinement
Similar structure data	2gkd-d 3fer-1 1ma3-d 5vfn-d 3zsf-2 4knw-3 2qop-d 5tyi-1 4pq0-d 4icg-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) 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: IDP91988

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#261 - Sep 2021 DNA-Sequencing Nanopores similarity (1) #22 - Oct 2001 Photosystem I similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #29 - May 2002 Penicillin-binding Proteins similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

Deposited unit

A: Phosphate-binding protein pstS 1

B: Phosphate-binding protein pstS 1

C: Phosphate-binding protein pstS 1

D: Phosphate-binding protein pstS 1

hetero molecules

113 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Phosphate-binding protein pstS 1

hetero molecules

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

2

B: Phosphate-binding protein pstS 1

hetero molecules

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

3

C: Phosphate-binding protein pstS 1

hetero molecules

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

4

D: Phosphate-binding protein pstS 1

hetero molecules

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

Unit cell

Length a, b, c (Å)	56.633, 76.501, 111.066
Angle α, β, γ (deg.)	90.00, 93.88, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Phosphate-binding protein pstS 1 / PBP 1 Mass: 28190.346 Da / Num. of mol.: 4 / Fragment: UNP residues 28-292 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: pstS1, SpneCM_010100007640, SP_1400 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97Q31, UniProt: Q8DPB1*PLUS
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1304 / 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: 2.13 Å³/Da / Density % sol: 42.22 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 25% (w/v) PEG 3350, 0.2 M magnesium chloride, 0.1 M Tris-Cl pH8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2012
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 1.68→25 Å / Num. all: 108303 / Num. obs: 107654 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / R_sym value: 0.055 / Net I/σ(I): 26.86
Reflection shell	Resolution: 1.68→1.71 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.25 / R_sym value: 0.432 / % possible all: 98.8

-
Processing

Software

Name	Version	Classification
HKL-3000		data collection
BALBES		phasing
PHENIX	(phenix.refine: 1.7.3_928)	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 1TWY

1twy

Resolution: 1.7→24.851 Å / SU ML: 0.24 / σ(F): 1.36 / Phase error: 21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2111	3395	1.83 %
R_work	0.1654	-	-
obs	0.1663	103395	90.5 %

Solvent computation

Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 51.302 Å² / k_sol: 0.36 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.0632 Å²	0 Å²	-1.9583 Å²
2-	-	1.0855 Å²	0 Å²
3-	-	-	-2.1488 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→24.851 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7784	0	13	1304	9101

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.02	8111
X-RAY DIFFRACTION	f_angle_d	1.681	11096
X-RAY DIFFRACTION	f_dihedral_angle_d	14.528	2957
X-RAY DIFFRACTION	f_chiral_restr	0.132	1301
X-RAY DIFFRACTION	f_plane_restr	0.008	1446

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 (%)
1.7-1.7243	0.3476	109	0.2938	7298	X-RAY DIFFRACTION	87
1.7243-1.75	0.3468	129	0.265	7255	X-RAY DIFFRACTION	87
1.75-1.7774	0.2868	141	0.2375	7363	X-RAY DIFFRACTION	87
1.7774-1.8065	0.2687	118	0.2351	7310	X-RAY DIFFRACTION	88
1.8065-1.8376	0.2424	137	0.2161	7395	X-RAY DIFFRACTION	88
1.8376-1.871	0.2675	150	0.1992	7376	X-RAY DIFFRACTION	88
1.871-1.907	0.2872	154	0.196	7391	X-RAY DIFFRACTION	89
1.907-1.9459	0.24	120	0.1915	7504	X-RAY DIFFRACTION	89
1.9459-1.9882	0.2825	147	0.1812	7450	X-RAY DIFFRACTION	89
1.9882-2.0345	0.2157	171	0.1719	7436	X-RAY DIFFRACTION	90
2.0345-2.0853	0.1854	127	0.1654	7516	X-RAY DIFFRACTION	90
2.0853-2.1417	0.2416	153	0.1709	7536	X-RAY DIFFRACTION	90
2.1417-2.2046	0.1913	132	0.1679	7609	X-RAY DIFFRACTION	90
2.2046-2.2758	0.2191	144	0.1568	7604	X-RAY DIFFRACTION	91
2.2758-2.357	0.1968	145	0.1522	7608	X-RAY DIFFRACTION	91
2.357-2.4513	0.1873	145	0.1527	7668	X-RAY DIFFRACTION	92
2.4513-2.5628	0.2526	152	0.1674	7666	X-RAY DIFFRACTION	92
2.5628-2.6977	0.1826	145	0.1817	7777	X-RAY DIFFRACTION	93
2.6977-2.8665	0.2667	135	0.1727	7703	X-RAY DIFFRACTION	92
2.8665-3.0875	0.2243	161	0.1764	7681	X-RAY DIFFRACTION	92
3.0875-3.3975	0.2037	140	0.1634	7720	X-RAY DIFFRACTION	92
3.3975-3.8875	0.1985	147	0.1394	7878	X-RAY DIFFRACTION	94
3.8875-4.8917	0.1435	145	0.1213	8042	X-RAY DIFFRACTION	96
4.8917-24.8535	0.1796	148	0.1577	7989	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	2.0576	-0.8272	1.3169	3.7613	-0.6418	3.0957	0.1286	0.1349	-0.3222	-0.3571	0.0163	0.3101	0.2561	-0.2182	-0.0791	0.1192	0.0235	-0.0067	0.0845	0.0014	0.1537	9.9526	24.5355	52.9883
2	2.5402	0.7965	0.2289	1.7657	1.2642	3.0625	0.067	-0.3187	-0.0278	0.1574	-0.131	0.068	0.0545	-0.2154	0.0486	0.063	-0.0103	0.0114	0.1214	0.0139	0.0973	-6.6694	37.7555	75.3002
3	1.1812	-0.5279	-0.448	1.5939	0.9657	2.4171	-0.0035	-0.0905	-0.0511	-0.0178	0.0623	-0.1384	0.0471	0.227	-0.0549	0.0605	0.001	0.0011	0.1027	0.0269	0.1309	14.2794	34.7941	63.5727
4	2.0932	0.6913	-0.1314	2.734	-0.9621	1.0667	-0.103	0.1727	-0.0679	-0.207	0.0198	-0.1152	0.1235	-0.0199	0.0799	0.0754	-0.0029	0.0102	0.0813	-0.0107	0.1011	10.1685	61.4662	55.0135
5	2.3771	0.0279	-0.5254	1.3239	0.9673	3.2967	-0.0156	-0.1008	0.0069	0.0152	-0.0287	0.0398	-0.052	-0.1207	0.0425	0.1217	-0.0158	-0.018	0.0782	0.0072	0.1127	-5.5534	78.0905	76.0341
6	1.374	-0.2744	-0.6862	1.6245	1.2774	2.0712	0.0099	-0.0557	0.0074	0.006	0.0219	-0.1934	-0.1447	0.1627	-0.0475	0.0911	-0.0251	-0.0126	0.0719	0.0301	0.1405	15.0458	73.4752	64.6636
7	4.2675	0.1043	-1.2224	1.2752	0.5342	2.0188	0.1676	-1.4596	1.9711	0.1879	0.4305	-0.0386	-0.2825	0.5844	-0.1859	0.2407	0.025	-0.0234	0.35	-0.2125	0.3676	32.0873	29.0021	102.0352
8	3.2901	0.7036	0.2109	2.2746	1.5984	3.4062	0.0246	-0.247	0.0811	-0.1265	-0.1079	0.0582	-0.2246	-0.0718	0.0694	0.2064	0.0123	-0.0325	0.1433	-0.0173	0.0842	5.141	14.3972	99.5578
9	4.5718	1.2496	0.8466	2.2303	1.9517	2.3068	-0.0511	0.2315	0.1278	-0.0253	0.1837	-0.2102	0.0375	0.3497	-0.1192	0.2018	0.0228	-0.004	0.2049	0.0361	0.1255	28.1264	18.2831	91.389
10	2.4256	-1.1014	1.4139	1.5702	-0.2055	2.6649	0.1761	0.1057	0.4346	0.0295	0.0122	-0.1467	-0.2682	-0.3041	-0.1358	0.172	0.0849	0.0628	0.2741	0.1026	0.186	30.4319	67.0897	99.5135
11	3.2635	0.641	-0.3474	1.9233	1.434	2.1627	0.1492	-0.2498	-0.0988	-0.1655	-0.2023	0.0688	-0.2547	0.1794	0.0372	0.2162	-0.0007	-0.0412	0.2085	0.0313	0.0923	3.3061	51.637	98.4292
12	3.327	1.4328	1.6299	1.7982	1.5787	1.4836	0.0874	0.4751	0.087	-0.0535	0.0476	-0.1527	0.0195	0.1156	-0.1146	0.1593	0.0576	0.0208	0.2932	0.0853	0.1237	26.1566	55.3556	90.7406

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A and resi 30:107
2	X-RAY DIFFRACTION	2	chain A and resi 108:213
3	X-RAY DIFFRACTION	3	chain A and resi 214:290
4	X-RAY DIFFRACTION	4	chain B and resi 28:107
5	X-RAY DIFFRACTION	5	chain B and resi 108:213
6	X-RAY DIFFRACTION	6	chain B and resi 214:289
7	X-RAY DIFFRACTION	7	chain C and resi 31:107
8	X-RAY DIFFRACTION	8	chain C and resi 108:213
9	X-RAY DIFFRACTION	9	chain C and resi 214:292
10	X-RAY DIFFRACTION	10	chain D and resi 31:107
11	X-RAY DIFFRACTION	11	chain D and resi 108:213
12	X-RAY DIFFRACTION	12	chain D and resi 214:289

-
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://pdbjlvh1.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

-
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

-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

-
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