PDB-3ncy: X-ray crystal structure of an arginine agmatine antiporter (AdiC)...

ID or keywords:

Entry

Database: PDB / ID: 3ncy

Title

X-ray crystal structure of an arginine agmatine antiporter (AdiC) in complex with a Fab fragment

Components

AdiC
Fab Heavy chain
Fab Light chain

Keywords

TRANSPORT PROTEIN / membrane protein complex with Fab fragment / arginine agmatine antiporter / virtual proton pump / APC superfamily / IMMUNE SYSTEM

Function / homology

Function and homology information

antiporter activity / amino acid transport / identical protein binding / plasma membrane
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 3.2 Å

Authors

Fang, Y. / Jayaram, H. / Shane, T. / Komalkova-Partensky, L. / Wu, F. / Williams, C. / Xiong, Y. / Miller, C.

Citation

Journal: Nature / Year: 2009
Title: Structure of a prokaryotic virtual proton pump at 3.2 A resolution.
Authors: Fang, Y. / Jayaram, H. / Shane, T. / Komalkova-Partensky, L. / Wu, F. / Williams, C. / Xiong, Y. / Miller, C.

History

Deposition	Jun 6, 2010	Deposition site: RCSB / Processing site: RCSB
Supersession	Aug 18, 2010	ID: 3HQK
Revision 1.0	Aug 18, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Jul 17, 2019	Group: Advisory / Data collection / Refinement description Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Nov 6, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3ncy.cif.gz	950.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3ncy.ent.gz	796 KB	Display	PDB format
PDBx/mmJSON format	3ncy.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/nc/3ncy ftp://data.pdbj.org/pub/pdb/validation_reports/nc/3ncy	HTTPS FTP

-
Related structure data

Similar structure data	7344 4kfm-d 6la7-d 2r4l-d 5msu-d 6la6-d 0602 6yvy-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	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: AdiC

B: AdiC

C: AdiC

D: AdiC

Q: Fab Heavy chain

P: Fab Heavy chain

W: Fab Light chain

S: Fab Light chain

281 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: AdiC

B: AdiC

P: Fab Heavy chain

S: Fab Light chain

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

2

C: AdiC

D: AdiC

Q: Fab Heavy chain

W: Fab Light chain

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

Unit cell

Length a, b, c (Å)	79.661, 104.149, 154.025
Angle α, β, γ (deg.)	81.96, 75.93, 73.73
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2
1	3
2	3
1	4
2	4

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	chain C and (resseq 11:174 or resseq 182:185 or resseq...
2	1	1	chain D and (resseq 11:174 or resseq 182:185 or resseq...
1	1	2	chain A and (resseq 10:174 or resseq 182:270 or resseq 275:316 or resseq 326:439 )
2	1	2	chain B and (resseq 10:174 or resseq 182:270 or resseq 275:316 or resseq 326:439 )
1	1	3	chain Q and (resseq 1:91 or resseq 93:133 or resseq 140:218 )
2	1	3	chain P and (resseq 1:91 or resseq 93:133 or resseq 140:218 )
1	1	4	chain W and (resseq 1:30 or resseq 36:150 or resseq 152:161 or resseq 163:216 )
2	1	4	chain S and (resseq 1:30 or resseq 36:150 or resseq 152:161 or resseq 163:216 )

NCS ensembles :

ID
1
2
3
4

#1: Protein	AdiC Mass: 46959.395 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: ADIC_SALTY / Plasmid: pASK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60066
#2: Antibody	Fab Heavy chain Mass: 23400.170 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: HYBRIDOMA
#3: Antibody	Fab Light chain Mass: 23191.629 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Cell: HYBRIDOMA
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 4.22 Å³/Da / Density % sol: 70.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 30-35% PEG 400, 100-200mM CaCl2, 100mM Glycine pH 9-9.5, vapor diffusion, hanging drop, temperature 293K PH range: 9-9.5

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	78	1
2	78	1
3	78	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	23-ID-B	1	0.97942
SYNCHROTRON	ALS	8.2.2	2	1.0809
SYNCHROTRON	NSLS	X29A	3	1.006

Detector

Type	ID	Detector	Date
MARMOSAIC 300 mm CCD	1	CCD	Jan 1, 2008
ADSC QUANTUM 315	2	CCD	Oct 29, 2008
	3

Radiation

ID	Protocol	Scattering type	Wavelength-ID
1	MAD	x-ray	1
2		x-ray	1
3		x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97942	1
2	1.0809	1
3	1.006	1

Reflection

Redundancy: 11.3 % / Av σ(I) over netI: 24.74 / Number: 696997 / R_merge(I) obs: 0.109 / Χ²: 1.84 / D res high: 2.98 Å / D res low: 50 Å / Num. obs: 61704 / % possible obs: 67.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
8.08	50	99	1	0.045	3.002	15
6.42	8.08	99.7	1	0.083	2.364	15.7
5.61	6.42	99.6	1	0.149	1.755	15.8
5.09	5.61	99.5	1	0.175	1.612	15.7
4.73	5.09	99.4	1	0.183	1.6	15.4
4.45	4.73	99.2	1	0.213	1.522	14.8
4.23	4.45	98.7	1	0.288	1.49	13.5
4.04	4.23	96.3	1	0.363	1.433	11.9
3.89	4.04	90.8	1	0.505	1.505	10.3
3.75	3.89	83.1	1	0.556	1.599	8.6
3.64	3.75	76.9	1	0.627	1.572	7.2
3.53	3.64	69.5	1	0.759	1.717	6.2
3.44	3.53	62.4	1		1.931	5.5
3.36	3.44	53	1	0.809	2.237	4.7
3.28	3.36	44.4	1		2.528	4.1
3.21	3.28	32.9	1		2.626	3.4
3.15	3.21	19.9	1		2.261	2.2
3.09	3.15	13.9	1		1.251	1.7
3.03	3.09	9.2	1		1.42	1.3
2.98	3.03	5.5	1	0.87	1.669	1.2

Reflection

Resolution: 2.99→50 Å / Num. obs: 90050 / % possible obs: 98.2 % / Redundancy: 3.7 % / R_merge(I) obs: 0.086 / Net I/σ(I): 11.4

Reflection shell

Resolution (Å)	Redundancy (%)	% possible all	R_merge(I) obs
2.99-3.04	3	94.1
3.04-3.1	3.3	97.4
3.1-3.16	3.5	97.9
3.16-3.22	3.7	98.7
3.22-3.29	3.8	98.7	0.859
3.29-3.37	3.9	98.8	0.733
3.37-3.45	3.8	98.7	0.596
3.45-3.54	3.9	98.9	0.465
3.54-3.65	3.8	99	0.36
3.65-3.77	3.9	99	0.312
3.77-3.9	3.8	98.7	0.258
3.9-4.06	3.9	99.2	0.185
4.06-4.24	3.9	99.1	0.133
4.24-4.47	3.8	99.2	0.103
4.47-4.75	3.8	99.1	0.084
4.75-5.11	3.8	99.3	0.074
5.11-5.63	3.8	99.3	0.072
5.63-6.44	3.8	99.4	0.065
6.44-8.11	3.7	99.1	0.052
8.11-50	3.5	90.8	0.046

-
Processing

Software

Name	Version	Classification
PHENIX	1.6.1_357	refinement
REFMAC		refinement
PDB_EXTRACT	3.1	data extraction
SCALEPACK		data scaling

Refinement

Resolution: 3.2→33.227 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.47 / σ(F): 1.96 / Phase error: 33.38 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.3118	3611	4.95 %
R_work	0.2816	-	-
obs	0.2831	72994	96.37 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 34.464 Å² / k_sol: 0.2 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-31.2028 Å²	-3.0605 Å²	-7.5455 Å²
2-	-	-38.0709 Å²	-2.8742 Å²
3-	-	-	-46.0303 Å²

Refine analyze

	Free	Obs
Luzzati coordinate error	0.69 Å	0.66 Å
Luzzati d res low	-	5 Å
Luzzati sigma a	1.16 Å	1.26 Å

Refinement step

Cycle: LAST / Resolution: 3.2→33.227 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18693	0	0	0	18693

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	19163
X-RAY DIFFRACTION	f_angle_d	0.883	26190
X-RAY DIFFRACTION	f_dihedral_angle_d	13.349	6496
X-RAY DIFFRACTION	f_chiral_restr	0.051	3115
X-RAY DIFFRACTION	f_plane_restr	0.005	3238

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	C	2941	X-RAY DIFFRACTION	POSITIONAL
1	2	D	2941	X-RAY DIFFRACTION	POSITIONAL	0.016
2	1	A	2977	X-RAY DIFFRACTION	POSITIONAL
2	2	B	2977	X-RAY DIFFRACTION	POSITIONAL	0.014
3	1	Q	1595	X-RAY DIFFRACTION	POSITIONAL
3	2	P	1595	X-RAY DIFFRACTION	POSITIONAL	0.024
4	1	W	1608	X-RAY DIFFRACTION	POSITIONAL
4	2	S	1608	X-RAY DIFFRACTION	POSITIONAL	0.015

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 (%)
3.2-3.2421	0.476	124	0.4086	2592	X-RAY DIFFRACTION	94
3.2421-3.2864	0.3808	136	0.386	2673	X-RAY DIFFRACTION	95
3.2864-3.3334	0.3573	138	0.361	2652	X-RAY DIFFRACTION	96
3.3334-3.3831	0.4094	118	0.3681	2622	X-RAY DIFFRACTION	95
3.3831-3.4359	0.378	114	0.3507	2652	X-RAY DIFFRACTION	95
3.4359-3.4921	0.3537	120	0.3461	2660	X-RAY DIFFRACTION	95
3.4921-3.5523	0.3393	132	0.3129	2636	X-RAY DIFFRACTION	96
3.5523-3.6168	0.3556	148	0.3151	2703	X-RAY DIFFRACTION	96
3.6168-3.6863	0.3353	137	0.3068	2615	X-RAY DIFFRACTION	95
3.6863-3.7614	0.3431	150	0.296	2623	X-RAY DIFFRACTION	96
3.7614-3.8431	0.3476	141	0.2952	2656	X-RAY DIFFRACTION	96
3.8431-3.9324	0.3517	132	0.2893	2605	X-RAY DIFFRACTION	95
3.9324-4.0305	0.2902	149	0.2614	2666	X-RAY DIFFRACTION	95
4.0305-4.1393	0.2808	130	0.2536	2695	X-RAY DIFFRACTION	97
4.1393-4.2609	0.2784	144	0.2376	2693	X-RAY DIFFRACTION	98
4.2609-4.3981	0.2648	144	0.2323	2702	X-RAY DIFFRACTION	98
4.3981-4.5549	0.2635	134	0.2248	2742	X-RAY DIFFRACTION	98
4.5549-4.7368	0.2308	159	0.2157	2686	X-RAY DIFFRACTION	98
4.7368-4.9517	0.2365	116	0.2088	2758	X-RAY DIFFRACTION	98
4.9517-5.2119	0.2708	144	0.2148	2707	X-RAY DIFFRACTION	99
5.2119-5.537	0.2675	151	0.2354	2703	X-RAY DIFFRACTION	99
5.537-5.9623	0.2816	147	0.2462	2746	X-RAY DIFFRACTION	99
5.9623-6.5581	0.2775	157	0.2449	2749	X-RAY DIFFRACTION	99
6.5581-7.4976	0.273	147	0.2411	2731	X-RAY DIFFRACTION	99
7.4976-9.4105	0.231	162	0.2226	2649	X-RAY DIFFRACTION	97
9.4105-33.2283	0.3208	137	0.297	2467	X-RAY DIFFRACTION	89

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	0.4308	-0.4305	0.337	0.77	-0.3028	0.403	0.3337	0.3098	-0.1575	-0.1957	-0.1623	0.2353	0.2782	0.165	-0.1248	0.3116	0.089	-0.1032	0.7796	0.3683	0.411	80.119	36.882	79.425
2	0.5015	-0.0882	0.065	0.5396	-0.0277	0.1299	0.0264	0.059	0.1143	0.4614	-0.1467	-0.0699	0.0231	0.069	-0.096	0.4519	-0.1031	0.0452	0.9988	0.5666	0.4193	91.0195	62.2223	108.0095
3	0.686	-0.1143	0.0131	0.992	0.0195	0.0132	0.242	0.5183	0.0521	-0.4349	-0.1549	0.3775	0.0183	0.0139	0.1341	0.0234	0.1296	-0.0458	0.0932	-0.1605	0.0745	16.3978	106.8538	-10.6522
4	0.6902	0.144	0.2068	0.1961	-0.0936	0.7164	-0.0932	0.1447	0.3754	0.0189	-0.0597	0.1356	-0.578	0.4097	-0.0265	0.243	-0.3575	0.0488	-0.015	-0.0332	0.2704	31.6085	132.9651	15.1271
5	0.0232	-0.0137	0.0354	0.0064	-0.0105	0.2895	0.0751	-0.3453	-0.134	0.0073	0.175	0.0259	-0.2017	-0.169	-0.1673	0.1327	0.1521	0.2525	0.7318	0.3363	0.5315	72.0796	84.7781	74.4678
6	0.0784	0.0191	-0.0818	0.1605	-0.0605	0.1401	0.097	0.1784	0.2153	0.1078	0.0329	0.2439	-0.1032	-0.1214	-0.1301	0.2537	0.1955	0.1714	0.7283	0.3986	0.6582	65.8995	103.2966	47.3078
7	0.0669	0.0846	-0.0318	0.3763	-0.0928	0.1173	0.2734	-0.0489	-0.0833	-0.076	-0.3949	-0.4553	0.0923	0.3754	0.1636	0.0519	0.1607	0.0302	0.9419	0.4278	0.573	43.2047	90.986	26.7197
8	0.0512	-0.0627	-0.0392	0.0948	0.0156	0.1734	-0.1635	-0.0324	-0.1271	0.0098	-0.0645	0.0787	0.0392	0.109	0.1767	0.5184	0.1962	0.0868	0.789	0.2864	1.0388	44.9725	60.7944	40.5419
9	0.2488	0.0443	-0.0544	0.0079	-0.0205	0.0804	0.0658	-0.1413	0.0211	0.0054	0.0161	-0.0107	-0.0752	0.0732	0.0489	-0.0808	-0.0461	0.1462	0.0453	-0.0901	0.0483	89.7755	80.2238	61.9741
10	0.5018	-0.1561	-0.1985	0.0868	-0.0142	0.2561	0.209	0.1491	0.4381	0.0351	0.0914	0.1268	-0.3297	-0.1599	-0.268	0.3364	0.1848	0.1953	0.2966	0.2571	0.6459	79.3854	111.0754	44.1176
11	0.0754	0.028	0.097	0.0884	0.0492	0.1239	0.1058	0.0307	-0.2254	0.0281	0.0949	-0.0625	0.0758	-0.0265	0.3609	-0.174	-0.0314	-0.0649	-0.5829	-0.4138	-0.0995	21.9703	86.9988	31.4408
12	0.0076	0.0225	0.0008	0.0714	-0.0287	0.103	-0.0207	-0.1172	-0.0227	0.0143	0.0636	0.0825	0.062	-0.0095	-0.061	0.4956	0.2558	0.0105	1.134	0.8498	1.0037	36.2299	61.3745	54.1573

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain A
2	X-RAY DIFFRACTION	2	chain B
3	X-RAY DIFFRACTION	3	chain C
4	X-RAY DIFFRACTION	4	chain D
5	X-RAY DIFFRACTION	5	chain P and resid 1:118
6	X-RAY DIFFRACTION	6	chain P and resid 119:217
7	X-RAY DIFFRACTION	7	chain Q and resid 1:118
8	X-RAY DIFFRACTION	8	chain Q and resid 119:216
9	X-RAY DIFFRACTION	9	chain S and resid 1:110
10	X-RAY DIFFRACTION	10	chain S and resid 111:216
11	X-RAY DIFFRACTION	11	chain W and resid 1:110
12	X-RAY DIFFRACTION	12	chain W and resid 111:216

-
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