PDB-4q4h: TM287/288 in its apo state

ID or keywords:

Entry

Database: PDB / ID: 4q4h

Title

TM287/288 in its apo state

Components

ABC transporter
Uncharacterized ABC transporter ATP-binding protein TM_0288

Keywords

HYDROLASE/TRANSPORT PROTEIN / ABC exporter / Multidrug efflux / ABC Transporter / Membrane Transporter / HYDROLASE-TRANSPORT PROTEIN complex

Function / homology

Function and homology information

ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function

Biological species

Thermotoga maritima (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.527 Å

Authors

Hohl, M. / Gruetter, M.G. / Seeger, M.A.

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter.
Authors: Hohl, M. / Hurlimann, L.M. / Bohm, S. / Schoppe, J. / Grutter, M.G. / Bordignon, E. / Seeger, M.A.

History

Deposition	Apr 14, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 16, 2014	Provider: repository / Type: Initial release
Revision 1.1	Jul 23, 2014	Group: Database references
Revision 1.2	Aug 20, 2014	Group: Database references
Revision 1.3	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.4	Feb 28, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4q4h.cif.gz	475.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4q4h.ent.gz	393.8 KB	Display	PDB format
PDBx/mmJSON format	4q4h.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4q4h_validation.pdf.gz	443.7 KB	Display	wwPDB validaton report
Full document	4q4h_full_validation.pdf.gz	476.6 KB	Display
Data in XML	4q4h_validation.xml.gz	40.1 KB	Display
Data in CIF	4q4h_validation.cif.gz	54.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q4/4q4h ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q4h	HTTPS FTP

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Related structure data

Related structure data	4q4aC 4q4jC 3qf4 C: citing same article (ref.)
Similar structure data	5mkk-d 5ta0-3 5tv4-d 6pam-1 4q4j-d 2dex-1 3b1u-1 2dew-1 6p6i-d 2dey-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#123 - Mar 2010 P-glycoprotein similarity (10) #95 - Nov 2007 Multidrug Resistance Transporters similarity (10)

Deposited unit

A: ABC transporter

B: Uncharacterized ABC transporter ATP-binding protein TM_0288

133 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)	214.640, 84.010, 114.110
Angle α, β, γ (deg.)	90.00, 93.27, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Protein	ABC transporter / ABC transporter / ATP-binding protein / Lipid A export ATP-binding/permease protein MsbA Mass: 65060.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0287, THEMA_03290, Tmari_0285 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC3
#2: Protein	Uncharacterized ABC transporter ATP-binding protein TM_0288 Mass: 67789.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0288 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WYC4
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.87 Å³/Da / Density % sol: 68.18 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 26 % (w/v) polyethylene glycol (PEG) 400, 50 mM Na-cacodylate, 50 mM CaCl2, 2.5 mM ADP and 3 mM MgCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction	Mean temperature: 90 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 9, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.527→29.512 Å / Num. all: 68156 / Num. obs: 59480 / % possible obs: 87.27 % / Observed criterion σ(F): -3

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Processing

Software

Name	Version	Classification
PHASER		phasing
PHENIX	(phenix.refine: 1.8_1069)	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.527→29.512 Å / SU ML: 0.42 / σ(F): 1.99 / Phase error: 34.63 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2904	3003	5.05 %
R_work	0.2367	-	-
obs	0.2395	59480	87.27 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.527→29.512 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9126	0	0	12	9138

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	9282
X-RAY DIFFRACTION	f_angle_d	0.922	12551
X-RAY DIFFRACTION	f_dihedral_angle_d	15.534	3480
X-RAY DIFFRACTION	f_chiral_restr	0.064	1489
X-RAY DIFFRACTION	f_plane_restr	0.004	1583

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 (%)
2.5267-2.5681	0.4751	31	0.317	600	X-RAY DIFFRACTION	20
2.5681-2.6124	0.3775	65	0.3191	1259	X-RAY DIFFRACTION	41
2.6124-2.6599	0.4261	108	0.3184	1776	X-RAY DIFFRACTION	59
2.6599-2.711	0.4061	127	0.2987	2207	X-RAY DIFFRACTION	72
2.711-2.7663	0.316	137	0.3046	2403	X-RAY DIFFRACTION	79
2.7663-2.8264	0.3717	141	0.3063	2627	X-RAY DIFFRACTION	86
2.8264-2.8921	0.369	142	0.2964	2786	X-RAY DIFFRACTION	91
2.8921-2.9643	0.3686	131	0.275	2933	X-RAY DIFFRACTION	95
2.9643-3.0444	0.3496	162	0.2762	3063	X-RAY DIFFRACTION	100
3.0444-3.1339	0.3032	152	0.2585	3069	X-RAY DIFFRACTION	100
3.1339-3.2349	0.3291	162	0.259	3087	X-RAY DIFFRACTION	100
3.2349-3.3504	0.3314	163	0.2612	3052	X-RAY DIFFRACTION	100
3.3504-3.4843	0.2745	151	0.255	3091	X-RAY DIFFRACTION	100
3.4843-3.6426	0.324	148	0.2474	3018	X-RAY DIFFRACTION	98
3.6426-3.8343	0.3125	179	0.2632	2949	X-RAY DIFFRACTION	96
3.8343-4.074	0.2695	147	0.222	3030	X-RAY DIFFRACTION	98
4.074-4.3876	0.2627	177	0.1862	3076	X-RAY DIFFRACTION	100
4.3876-4.8274	0.2479	167	0.1658	3074	X-RAY DIFFRACTION	100
4.8274-5.522	0.2356	166	0.1869	3111	X-RAY DIFFRACTION	100
5.522-6.9421	0.3019	171	0.2486	3111	X-RAY DIFFRACTION	100
6.9421-29.5135	0.2174	176	0.2167	3155	X-RAY DIFFRACTION	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	4.4091	-0.9762	-2.3979	0.8828	0.4962	2.4632	0.1879	-0.1566	0.5268	0.0286	0.1222	-0.0762	-0.2723	0.345	-0.3209	0.5376	-0.1223	0.0433	0.3453	-0.071	0.5147	-29.37	18.3857	32.1172
2	1.9442	0.19	-1.3077	0.8475	-0.3769	1.1495	0.0118	1.5077	0.5222	-0.1129	-0.0463	0.622	0.2036	-0.9681	0.0918	0.8433	-0.232	-0.1336	1.6001	0.0076	0.6845	-55.3568	7.4723	15.1686
3	7.783	-2.7264	-6.5362	5.2841	1.8951	6.4599	-0.1519	1.8799	0.269	-0.0003	0.1516	-0.2802	-0.1397	-0.9397	0.1265	0.8101	-0.1659	0.0774	1.024	-0.0672	0.6865	-20.6079	16.18	11.2187
4	9.2432	-0.0253	-7.7223	1.7325	0.1371	8.6262	0.5571	0.0942	-0.1013	-0.6124	-0.6771	-0.1342	-1.4528	-0.2018	-0.0029	0.7365	0.0172	0.186	0.5001	0.0149	0.7738	-52.2506	26.9026	39.3342
5	5.4536	2.2517	0.7655	3.9659	1.077	4.368	0.0198	0.6075	0.3573	-0.3473	0.2291	0.2833	-0.5156	-0.2532	-0.2228	0.6339	0.0899	0.1824	0.431	0.0618	0.8595	-75.9868	30.3723	57.5754
6	2.4402	-1.6682	-0.5432	2.7063	0.7637	1.4104	-0.0377	0.1229	-0.5085	-0.3362	0.0059	-0.2368	0.3132	-0.0158	-0.0183	0.878	-0.0178	0.2448	0.4471	0.0247	0.9085	-69.0701	7.1239	62.112
7	9.458	2.9008	-2.5078	2.3493	-1.2209	2.8202	0.5297	-0.2735	-1.0908	0.7878	-0.9398	0.6623	0.3503	-1.2191	0.0348	0.6833	-0.0591	0.1161	0.8372	-0.0308	1.4311	-83.7923	8.4866	64.7454
8	8.0845	2.1718	1.9452	5.3237	0.2615	6.4442	-0.1774	0.4214	0.7549	-0.0235	-0.0217	1.5241	0.1059	-1.4703	0.2203	0.5103	-0.0429	-0.0121	0.9492	0.0395	1.1676	-93.9525	20.8491	55.0752
9	1.7748	0.4152	2.9938	2.3804	3.3017	8.023	-0.1482	1.0944	-1.2578	0.4153	0.4737	0.0164	0.969	0.0861	-0.3225	1.1651	-0.536	0.3615	1.2494	-0.5449	1.2674	-48.8521	-15.2747	22.5978
10	4.3457	0.9684	-1.1075	1.6624	-0.2484	0.7251	-0.1648	0.7188	0.0454	-0.5607	0.0956	0.0148	0.3711	-0.4638	0.134	0.9692	-0.3025	0.0043	1.3155	-0.2832	0.5988	-41.5761	-2.2621	11.2398
11	8.9741	-0.0536	-0.0565	2.9401	0.6344	3.3996	0.0441	1.0953	-0.213	-0.8445	-0.2297	-0.1857	0.234	-0.3555	0.234	1.0498	-0.0454	0.2054	0.6058	-0.0915	0.6263	-23.2187	-8.003	14.7542
12	6.038	-1.8211	-2.7879	1.4633	0.5309	2.3109	-0.3087	0.1	-0.243	0.2444	0.1825	0.4596	0.2686	-0.0142	0.1556	0.6637	-0.0635	0.1036	0.3756	-0.0089	0.6492	-38.8238	6.9367	43.305
13	2.9642	0.132	-1.2767	0.8792	-0.0271	1.2108	-0.1187	0.3515	-0.4901	-0.2492	-0.0625	0.1978	0.4697	-0.3382	0.0728	0.9322	-0.2888	0.0517	0.9261	-0.1694	0.7677	-55.4303	-11.1523	27.2703
14	2.4973	0.5656	-1.6793	1.6555	-0.3395	1.8257	-0.314	1.1808	-0.3768	-0.3395	-0.0034	0.075	0.3892	-1.4315	0.1584	0.865	-0.4526	-0.1251	1.8908	-0.1848	1.1175	-87.551	-0.4907	29.5076
15	0.9621	-1.6435	-0.2586	5.0629	-0.5529	2.4753	-0.3341	0.6003	0.0397	0.361	-0.0745	-0.0313	-0.1513	-0.906	0.3872	0.6286	-0.3027	-0.1699	1.495	-0.1382	1.0005	-91.3379	7.7279	34.5769
16	3.4723	-1.4098	-0.1867	5.0397	1.529	4.4216	-0.7576	0.3911	-0.4535	0.6652	0.4039	1.1586	0.6098	-0.94	0.2523	1.0551	-0.4316	0.211	1.4162	-0.2112	1.2469	-97.9551	-3.8604	49.3714

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid -2:163)
2	X-RAY DIFFRACTION	2	(chain A and resid 164:255)
3	X-RAY DIFFRACTION	3	(chain A and resid 256:296)
4	X-RAY DIFFRACTION	4	(chain A and resid 297:316)
5	X-RAY DIFFRACTION	5	(chain A and resid 317:402)
6	X-RAY DIFFRACTION	6	(chain A and resid 403:498)
7	X-RAY DIFFRACTION	7	(chain A and resid 499:520)
8	X-RAY DIFFRACTION	8	(chain A and resid 521:569)
9	X-RAY DIFFRACTION	9	(chain B and resid 10:35)
10	X-RAY DIFFRACTION	10	(chain B and resid 36:151)
11	X-RAY DIFFRACTION	11	(chain B and resid 152:185)
12	X-RAY DIFFRACTION	12	(chain B and resid 186:280)
13	X-RAY DIFFRACTION	13	(chain B and resid 281:379)
14	X-RAY DIFFRACTION	14	(chain B and resid 380:490)
15	X-RAY DIFFRACTION	15	(chain B and resid 491:535)
16	X-RAY DIFFRACTION	16	(chain B and resid 536:592)

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