PDB-4r1i: Structure and Function of Neisseria gonorrhoeae MtrF Illuminates ...

ID or keywords:

Entry

Database: PDB / ID: 4r1i

Title

Structure and Function of Neisseria gonorrhoeae MtrF Illuminates a Class of Antimetabolite Efflux Pumps

Components

Aminobenzoyl-glutamate transporter

Keywords

MEMBRANE PROTEIN / transmembrane protein

Function / homology

AbgT, Proteobacteria / secondary active p-aminobenzoyl-glutamate transmembrane transporter activity / p-aminobenzoyl-glutamate transmembrane transport / p-Aminobenzoyl-glutamate transport protein AbgT / AbgT putative transporter family / membrane / : / Antibiotic resistance efflux pump component

Function and homology information

Biological species

Neisseria gonorrhoeae FA19 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.959 Å

Authors

Su, C.-C. / Bolla, J.R. / Yu, E.W.

Citation

Journal: Cell Rep / Year: 2015
Title: Structure and Function of Neisseria gonorrhoeae MtrF Illuminates a Class of Antimetabolite Efflux Pumps.
Authors: Su, C.C. / Bolla, J.R. / Kumar, N. / Radhakrishnan, A. / Long, F. / Delmar, J.A. / Chou, T.H. / Rajashankar, K.R. / Shafer, W.M. / Yu, E.W.

History

Deposition	Aug 6, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 29, 2015	Group: Database references
Revision 1.2	Feb 28, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4r1i.cif.gz	401 KB	Display	PDBx/mmCIF format
PDB format	pdb4r1i.ent.gz	339.3 KB	Display	PDB format
PDBx/mmJSON format	4r1i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4r1i_validation.pdf.gz	440.7 KB	Display	wwPDB validaton report
Full document	4r1i_full_validation.pdf.gz	473.1 KB	Display
Data in XML	4r1i_validation.xml.gz	37.6 KB	Display
Data in CIF	4r1i_validation.cif.gz	50.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r1/4r1i ftp://data.pdbj.org/pub/pdb/validation_reports/r1/4r1i	HTTPS FTP

-
Related structure data

Related structure data	4r0c
Similar structure data	4ff3-1 2po4-d 5vad-d 4ff2-1 3c46-2 2c8a-d 7b3b-d 3c3l-2 7bv2-d 6xqb-d 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

Deposited unit

A: Aminobenzoyl-glutamate transporter

B: Aminobenzoyl-glutamate transporter

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	120.766, 120.766, 233.897
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	170
Space group name H-M	P6₅

#1: Protein	Aminobenzoyl-glutamate transporter Mass: 56170.199 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae FA19 (bacteria) / Strain: FA19 / Gene: NGEG_01484 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: D1DA20, UniProt: Q9RNX2*PLUS

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.38 Å³/Da / Density % sol: 71.94 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 30% PEG400, 0.05M Mg(Ac)2, 0.1M NaAc(5.0), and 3% glycerol, pH 7.5, vapor diffusion, temperature 298K

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.98 Å

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 26, 2013

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 3.95→50 Å / Num. obs: 16468 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / B_iso Wilson estimate: 202.86 Å² / R_merge(I) obs: 0.071 / Net I/σ(I): 7.4

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
3.95-4.11	2.2	0.921	1	84.5
4.11-4.29	2.3	0.519	1	91.3
4.29-4.52	2.3	0.356	1	93.8
4.52-4.8	2.6	0.283	1	97.6
4.8-5.17	2.7	0.278	1	99.8
5.17-5.7	2.7	0.187	1	99.3
5.7-6.52	2.5	0.138	1	98.4
6.52-8.21	2.5	0.074	1	96.3
8.21-50	2.3	0.05	1	95.2

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.14	data extraction
HKL-2000		data collection
HKL-2000		data reduction
MLPHARE		phasing

Refinement

Method to determine structure:

SAD / Resolution: 3.959→47.74 Å / SU ML: 0.94 / σ(F): 1.34 / Phase error: 53.05 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.3383	869	5.3 %
R_work	0.3108	-	-
obs	0.3124	16382	97.36 %
all	-	16382	-

Solvent computation

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

Displacement parameters

B_iso mean: 232.14 Å²

Refinement step

Cycle: LAST / Resolution: 3.959→47.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7684	0	0	0	7684

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7883
X-RAY DIFFRACTION	f_angle_d	1	10755
X-RAY DIFFRACTION	f_dihedral_angle_d	17.649	2721
X-RAY DIFFRACTION	f_chiral_restr	0.063	1290
X-RAY DIFFRACTION	f_plane_restr	0.005	1321

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 (%)
3.9592-4.2071	0.549	152	0.4017	2388	X-RAY DIFFRACTION	91
4.2071-4.5317	0.4191	137	0.3245	2625	X-RAY DIFFRACTION	98
4.5317-4.9873	0.3436	142	0.2803	2638	X-RAY DIFFRACTION	100
4.9873-5.7079	0.4261	157	0.3059	2641	X-RAY DIFFRACTION	99
5.7079-7.1874	0.4531	130	0.3947	2625	X-RAY DIFFRACTION	99
7.1874-47.7431	0.2827	151	0.287	2596	X-RAY DIFFRACTION	97

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	0.4997	-0.5435	-0.2382	0.8034	0.2935	0.0733	-0.161	-0.6738	-1.2452	-0.1042	0.2639	1.0555	0.9562	-0.0937	0.1099	0.5895	2.1866	0.1568	0.9769	-0.1744	0.717	13.7754	49.4281	28.7986
2	1.1981	0.9803	-0.2252	1.7281	-0.896	0.8507	0.6809	-0.2285	0.9728	0.9963	1.2925	0.8864	-0.2809	0.1118	2.3708	0.6968	1.7806	0.3022	1.118	-1.9426	0.6308	41.4656	61.0366	34.5016
3	0.5837	0.6347	-0.5029	0.4706	-0.262	1.28	0.4221	0.3865	-0.4708	0.0921	0.5291	-0.2413	0.4468	0.2009	1.2053	2.1174	1.1024	0.5915	1.9594	-0.5782	0.4471	42.3275	68.6626	32.4123
4	0.9123	-0.8624	1.0145	2.2527	0.5171	2.2114	0.8018	-0.3409	0.2173	-0.5332	0.6852	-1.6483	0.4165	-0.8093	2.5202	0.0597	0.8716	-0.161	0.8338	-0.2157	0.375	25.0365	56.8468	29.051
5	0.1415	-0.0879	-0.0148	0.4062	-0.0654	0.0398	-0.6731	-0.0521	0.4023	0.3459	0.3192	-0.2326	-1.0178	-0.3786	-0.0621	2.7275	1.8464	-0.339	1.2113	0.2639	0.6748	34.3662	55.1174	42.5499
6	1.4678	0.8294	0.1744	0.4654	0.0941	0.0476	0.0371	0.5031	-0.7596	0.0283	-0.2163	-0.7729	-0.2471	0.7928	-0.2315	0.6529	1.5357	0.3598	1.5873	0.1646	0.6801	36.8199	66.8371	-5.1668
7	0.0973	0.2182	-0.1448	0.6946	-0.387	0.2148	0.3298	-1.1291	-0.1499	1.0112	0.0976	-0.364	-0.554	1.1148	-0.0809	1.381	0.1328	-0.077	3.0809	-0.9982	2.3904	13.7509	79.507	-0.7141
8	0.0281	0.0093	-0.1567	0.0533	-0.2519	1.1627	-0.574	-0.1614	0.6186	-0.1086	-0.3304	-0.1373	0.8704	0.5116	-0.9223	-0.6928	0.9914	-1.0125	0.1013	0.3534	0.5169	22.3284	52.9031	10.6917
9	0.13	-0.0353	-0.1232	0.2232	-0.1707	0.2608	0.2384	0.5885	-0.1061	0.3339	0.4874	-0.4564	0.1124	0.5221	0.3885	1.324	0.7664	-0.3874	0.8206	-1.7131	2.2117	33.3297	30.4639	-6.9941
10	1.2872	1.0532	-0.6208	0.891	-0.0854	3.8445	1.2414	0.3579	0.4921	0.2064	1.1883	1.8249	0.4518	-0.6973	3.4205	0.2289	0.2953	-1.0759	0.4371	0.569	1.5792	17.9805	49.4162	-4.6799
11	0.5234	-0.0087	0.5544	0.272	-0.0764	0.5013	0.0788	-0.8198	0.2435	0.4527	0.5126	-0.9838	-0.0593	-1.1788	0.2739	1.248	1.5316	-1.102	3.3807	-0.1879	-1.1608	30.8344	27.6771	-4.2299
12	4.4737	0.0399	1.0291	0.8505	1.4332	2.7421	2.5002	0.2218	-1.2941	-0.7045	-0.0583	-0.5605	-0.826	0.0917	3.7661	0.0491	1.514	-0.1399	1.0241	-0.1219	0.49	20.076	53.4388	-0.6332
13	0.3672	-0.1706	0.1245	0.1815	0.1324	-0.1465	-0.3488	0.431	-0.1238	0.7187	0.3578	-0.8386	1.5918	0.2498	-0.8218	-0.3189	-0.291	-1.3772	2.5284	-1.7705	0.8937	32.7746	45.0414	-14.2051

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 10 through 111 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 112 through 214 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 215 through 314 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 315 through 432 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 433 through 516 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 11 through 44 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 45 through 84 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 85 through 111 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 112 through 179 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 180 through 231 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 232 through 292 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 293 through 453 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 454 through 516 )

-
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

-
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