PDB-3quj: Crystal structure of the phosphonate binding protein, PhnD, from ...

ID or keywords:

Entry

Database: PDB / ID: 3quj

Title

Crystal structure of the phosphonate binding protein, PhnD, from Escherichia coli

Components

PhnD, subunit of alkylphosphonate ABC transporter

Keywords

TRANSPORT PROTEIN / Bind and transport of phosphonates

Function / homology

Function and homology information

organic phosphonate transport / ATP-binding cassette (ABC) transporter complex / transmembrane transport
Similarity search - Function

Biological species

Escherichia coli UTI89 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Alicea, I. / Schreiter, E.R.

Citation

Journal: J.Mol.Biol. / Year: 2011
Title: Structure of the Escherichia coli Phosphonate Binding Protein PhnD and Rationally Optimized Phosphonate Biosensors.
Authors: Alicea, I. / Marvin, J.S. / Miklos, A.E. / Ellington, A.D. / Looger, L.L. / Schreiter, E.R.

History

Deposition	Feb 24, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 12, 2011	Provider: repository / Type: Initial release
Revision 1.1	Dec 21, 2011	Group: Database references

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3quj.cif.gz	450.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3quj.ent.gz	388.8 KB	Display	PDB format
PDBx/mmJSON format	3quj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	3quj_validation.pdf.gz	460.4 KB	Display	wwPDB validaton report
Full document	3quj_full_validation.pdf.gz	475.2 KB	Display
Data in XML	3quj_validation.xml.gz	42.8 KB	Display
Data in CIF	3quj_validation.cif.gz	60.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qu/3quj ftp://data.pdbj.org/pub/pdb/validation_reports/qu/3quj	HTTPS FTP

-
Related structure data

Related structure data	3p7iC 3qk6C 3s4uC C: citing same article (ref.)
Similar structure data	3qk6-d 3p7i-1 6kyr-d 6kyq-d 4yzg-d 6le5-2 6yt6-d 6epm-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 - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1)

Deposited unit

A: PhnD, subunit of alkylphosphonate ABC transporter

B: PhnD, subunit of alkylphosphonate ABC transporter

C: PhnD, subunit of alkylphosphonate ABC transporter

D: PhnD, subunit of alkylphosphonate ABC transporter

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

1

A: PhnD, subunit of alkylphosphonate ABC transporter

B: PhnD, subunit of alkylphosphonate ABC transporter

defined by author&software
72.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: PhnD, subunit of alkylphosphonate ABC transporter

D: PhnD, subunit of alkylphosphonate ABC transporter

defined by author&software
72.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.768, 64.399, 107.688
Angle α, β, γ (deg.)	90.00, 93.52, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	PhnD, subunit of alkylphosphonate ABC transporter Mass: 36136.715 Da / Num. of mol.: 4 / Fragment: UNP residues 27-338 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli UTI89 (bacteria) / Strain: UTI89 / UPEC / Gene: phnD, UTI89_C4699 / Plasmid: pRSET / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Crystal Express / References: UniProt: Q1R3F7
#2: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 4 / Source method: obtained synthetically
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.91 Å³/Da / Density % sol: 35.6 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Magnesium chloride hexahydrate, 0.1M Bis-tris, 25%(w/v) PEG 3,350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction	Mean temperature: 298 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
Detector	Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 19, 2009
Radiation	Monochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97929 Å / Relative weight: 1
Reflection	Resolution: 2.2→28.9 Å / Num. all: 55563 / Num. obs: 55007 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software

Name	Version	Classification
SPEC		data collection
PHASER	for MR	phasing
REFMAC	5.5.0072	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→28.9 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.878 / SU B: 16.498 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.265 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2764	2798	5.1 %	RANDOM
R_work	0.20213	-	-	-
all	0.20586	55563	-	-
obs	0.20586	52190	98.8 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 24.347 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.81 Å²	0 Å²	0.22 Å²
2-	-	1.86 Å²	0 Å²
3-	-	-	-1.03 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→28.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9212	0	20	201	9433

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	9452
X-RAY DIFFRACTION	r_angle_refined_deg	1.624	1.958	12818
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.693	5	1179
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	42.987	25.76	434
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.555	15	1660
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.761	15	36
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	1425
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	7136
X-RAY DIFFRACTION	r_mcbond_it	0.816	1.5	5885
X-RAY DIFFRACTION	r_mcangle_it	1.456	2	9479
X-RAY DIFFRACTION	r_scbond_it	2.595	3	3567
X-RAY DIFFRACTION	r_scangle_it	3.903	4.5	3333

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.32	182	-
R_work	0.221	3780	-
obs	-	-	98.26 %

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	2.2163	-0.2455	-0.1027	0.4726	-0.2115	0.745	-0.029	0.2975	-0.1375	-0.0369	-0.0634	0.0027	0.0123	-0.0158	0.0923	0.0112	0.0013	0.0028	0.0432	-0.0194	0.0191	-24.519	11.454	3.467
2	1.729	-0.2191	-0.0049	0.117	-0.0523	0.288	-0.025	-0.1292	0.0094	0.0087	0.0084	-0.0087	0.0207	-0.0417	0.0165	0.0129	-0.0015	0.0067	0.0191	-0.0014	0.0051	-36.443	15.497	17.698
3	1.4154	0.0572	-0.0941	0.2342	-0.1857	0.6033	-0.0763	-0.0526	0.0559	-0.0322	0.0463	-0.0147	-0.0013	-0.0886	0.0299	0.016	0.0099	-0.0045	0.0333	-0.0116	0.0052	-45.023	19.172	13.862
4	0.3522	0.214	0.1171	0.1983	-0.0128	0.4959	0.0228	-0.036	0.0581	-0.004	-0.0215	0.0236	-0.0147	-0.0395	-0.0013	0.0151	0.0079	0.0118	0.0188	-0.0017	0.0155	-22.93	15.201	21.698
5	12.6526	-1.8663	-6.0804	0.3281	0.8722	2.9392	0.3258	0.5568	0.2203	-0.014	-0.1917	-0.0239	-0.1877	-0.2226	-0.134	0.0494	-0.0494	0.0355	0.2119	-0.0027	0.0397	-5.563	23.697	29.703
6	1.2225	0.096	0.0029	0.1934	-0.087	0.3016	-0.0663	-0.0331	0.0135	0.0297	0.0158	-0.0112	0.0387	0.0348	0.0505	0.0308	0.0131	0.0071	0.0101	0.0057	0.0086	-0.86	14.013	48.434
7	0.9294	-0.0503	-0.091	0.2042	0.07	0.3102	-0.0568	-0.0271	0.0896	0.0165	0.037	-0.0272	0.042	0.0435	0.0197	0.0093	0.0071	-0.0024	0.0102	-0.0028	0.0159	5.315	16.994	45.28
8	0.1876	-0.0504	0.0661	0.3707	0.1012	0.1819	0.0099	0.0737	0.0565	0.0539	-0.033	-0.0469	0.0462	0.021	0.0231	0.0225	0.0017	-0.0018	0.0429	0.0158	0.0264	-2.503	14.562	33
9	0.6935	0.2189	1.084	0.0887	0.3646	1.7298	-0.1399	-0.678	0.2333	-0.1341	-0.1356	-0.0432	-0.4139	-0.9812	0.2756	0.4606	-0.0887	0.3952	0.9063	-0.4253	0.777	-23.731	23.48	28.913
10	1.1192	0.2016	-0.0442	0.1315	-0.0011	0.9882	0.0018	-0.0646	-0.1444	0.0198	0.023	-0.0241	0.0267	0.049	-0.0249	0.0108	0.0122	0.0051	0.0208	0.0115	0.0249	-5.821	46.138	14.279
11	0.6343	0.2372	0.0068	0.1118	-0.0135	0.8859	-0.024	0.0108	-0.0957	-0.0097	0.0208	-0.0422	0.0191	0.0406	0.0033	0.0154	0.0055	0.0155	0.0161	-0.0018	0.026	-7.889	49.314	8.698
12	0.4822	0.2116	0.4177	0.483	-0.0866	1.2604	-0.0174	-0.1295	0.0492	0.0309	0.0572	0.1023	0.0116	-0.1725	-0.0398	0.0136	0.0184	0.0093	0.0689	0.0108	0.0277	-15.869	49.166	18.366
13	0.9776	-1.7175	-2.2173	9.1515	5.7102	5.611	0.0215	0.159	0.0204	-0.1101	0.0788	-0.1266	-0.0546	-0.3447	-0.1004	0.0046	-0.0255	-0.0064	0.2244	0.0561	0.0207	-32.105	46.155	15.12
14	1.8724	-0.5359	0.4109	0.3798	0.676	5.6943	0.0833	0.2424	0.056	-0.0115	-0.0979	0.0654	-0.0706	-0.0936	0.0145	0.0112	0.0087	0.02	0.0583	0.0044	0.0596	-57.471	48.118	23.67
15	1.0141	-0.2134	0.342	0.3638	0.1573	1.3852	0.0047	-0.0275	-0.0465	0.0002	0.015	-0.0148	0.0221	0.1177	-0.0196	0.01	-0.0138	0.0029	0.0402	-0.0028	0.0051	-46.489	45.553	40.754
16	1.091	-0.0544	0.0332	0.0929	0.3848	1.8528	-0.0257	0.1847	0.1919	0.0002	0.0029	0.0029	-0.0675	0.0595	0.0227	0.0214	-0.0081	0.0068	0.0398	0.0337	0.0422	-50.269	52.846	32.021
17	1.1452	0.1771	-0.6827	0.1952	0.026	0.5114	-0.0149	0.0452	-0.137	0.0041	-0.0332	-0.0681	0.0159	-0.0467	0.048	0.0086	0.0135	0.0072	0.112	0.0345	0.039	-31.195	45.787	30.928

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 55
2	X-RAY DIFFRACTION	2	A	56 - 136
3	X-RAY DIFFRACTION	3	A	137 - 202
4	X-RAY DIFFRACTION	4	A	203 - 301
5	X-RAY DIFFRACTION	5	A	302 - 312
6	X-RAY DIFFRACTION	6	B	5 - 116
7	X-RAY DIFFRACTION	7	B	117 - 230
8	X-RAY DIFFRACTION	8	B	231 - 300
9	X-RAY DIFFRACTION	9	B	301 - 312
10	X-RAY DIFFRACTION	10	C	5 - 126
11	X-RAY DIFFRACTION	11	C	127 - 226
12	X-RAY DIFFRACTION	12	C	227 - 289
13	X-RAY DIFFRACTION	13	C	290 - 304
14	X-RAY DIFFRACTION	14	D	5 - 35
15	X-RAY DIFFRACTION	15	D	36 - 156
16	X-RAY DIFFRACTION	16	D	157 - 241
17	X-RAY DIFFRACTION	17	D	242 - 312

-
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