PDB-5gko: Crystal structure of tripartite-type ABC transporter, MacB from A...

ID or keywords:

Entry

Database: PDB / ID: 5gko

Title

Crystal structure of tripartite-type ABC transporter, MacB from Acinetobacter baumannii

Components

Macrolide export ATP-binding/permease protein MacB

Keywords

MEMBRANE PROTEIN / Multi-drug / efflux transporter / ABC transporter / Drug exporter

Function / homology

Function and homology information

Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / response to antibiotic / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3.393 Å

Authors

Murakami, S. / Okada, U. / Yamashita, E.

Funding support

Japan, 1items

Citation

Journal: Nat Commun / Year: 2017
Title: Crystal structure of tripartite-type ABC transporter MacB from Acinetobacter baumannii.
Authors: Okada, U. / Yamashita, E. / Neuberger, A. / Morimoto, M. / van Veen, H.W. / Murakami, S.

History

Deposition	Jul 4, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 15, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5gko.cif.gz	504.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5gko_validation.pdf.gz	447.5 KB	Display	wwPDB validaton report
Full document	5gko_full_validation.pdf.gz	475.6 KB	Display
Data in XML	5gko_validation.xml.gz	46 KB	Display
Data in CIF	5gko_validation.cif.gz	61.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gk/5gko ftp://data.pdbj.org/pub/pdb/validation_reports/gk/5gko	HTTPS FTP

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Related structure data

Related structure data	5ws4C C: citing same article (ref.)
Similar structure data	5ws4-d 5xu1-d 7arh-d 2a1d-d 5kyu-d 4eo4-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#123 - Mar 2010 P-glycoprotein similarity (5) #95 - Nov 2007 Multidrug Resistance Transporters similarity (5)

Deposited unit

A: Macrolide export ATP-binding/permease protein MacB

B: Macrolide export ATP-binding/permease protein MacB

147 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)	229.148, 229.148, 155.644
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Macrolide export ATP-binding/permease protein MacB Mass: 73304.062 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: macB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A0D8G707, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
Nonpolymer details	Authors observed nucleotide binding in the Walker-A regions of the nucleotide binding domains. The ...Authors observed nucleotide binding in the Walker-A regions of the nucleotide binding domains. The electron density observed cannot be assigned to ATP or ADP due to limited resolution. Thus Authors decided not to deposit any hetero-atoms for bound nucleotides to avoid uncertainty.

#1: Protein

Macrolide export ATP-binding/permease protein MacB

Mass: 73304.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Acinetobacter baumannii (bacteria) / Gene: macB / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A0D8G707, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

Nonpolymer details

Authors observed nucleotide binding in the Walker-A regions of the nucleotide binding domains. The ...

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 6.97 Å³/Da / Density % sol: 82.35 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 1.2M Sodium Citric acid, 0.1M HEPES, 0.1M Sodium Chloride

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.97869 Å
Detector	Type: MAR scanner 300 mm plate / Detector: CCD / Date: Oct 31, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97869 Å / Relative weight: 1
Reflection	Resolution: 3.393→50 Å / Num. obs: 57248 / % possible obs: 99.6 % / Redundancy: 8.2 % / Net I/σ(I): 28.2
Reflection shell	Resolution: 3.4→3.46 Å / Redundancy: 8.4 % / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3.393→43.963 Å / SU ML: 0.43 / Cross valid method: NONE / σ(F): 0 / Phase error: 30.63

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2547	2906	5.08 %	0.2547
R_work	0.2226	-	-	-
obs	0.2241	57248	99.25 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 3.393→43.963 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9770	0	0	0	9770

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	9948
X-RAY DIFFRACTION	f_angle_d	0.866	13496
X-RAY DIFFRACTION	f_dihedral_angle_d	8.443	6012
X-RAY DIFFRACTION	f_chiral_restr	0.051	1632
X-RAY DIFFRACTION	f_plane_restr	0.005	1746

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 (%)
3.3935-3.4491	0.4264	133	0.3833	2477	X-RAY DIFFRACTION	96
3.4491-3.5086	0.3949	157	0.3413	2546	X-RAY DIFFRACTION	100
3.5086-3.5723	0.3454	121	0.3142	2566	X-RAY DIFFRACTION	100
3.5723-3.641	0.3016	133	0.2942	2589	X-RAY DIFFRACTION	100
3.641-3.7153	0.3362	119	0.2831	2596	X-RAY DIFFRACTION	100
3.7153-3.796	0.3	152	0.2607	2548	X-RAY DIFFRACTION	100
3.796-3.8843	0.2914	135	0.2441	2563	X-RAY DIFFRACTION	100
3.8843-3.9814	0.2626	157	0.2351	2547	X-RAY DIFFRACTION	100
3.9814-4.0889	0.2462	119	0.2157	2612	X-RAY DIFFRACTION	100
4.0889-4.2092	0.2518	145	0.2161	2559	X-RAY DIFFRACTION	100
4.2092-4.3449	0.2622	133	0.2035	2588	X-RAY DIFFRACTION	100
4.3449-4.5	0.2238	146	0.1852	2587	X-RAY DIFFRACTION	100
4.5-4.68	0.2155	150	0.1745	2564	X-RAY DIFFRACTION	100
4.68-4.8928	0.217	119	0.1763	2613	X-RAY DIFFRACTION	100
4.8928-5.1503	0.2371	144	0.1977	2596	X-RAY DIFFRACTION	100
5.1503-5.4725	0.2158	131	0.2074	2613	X-RAY DIFFRACTION	100
5.4725-5.8941	0.2576	126	0.2191	2651	X-RAY DIFFRACTION	100
5.8941-6.4856	0.2383	151	0.227	2609	X-RAY DIFFRACTION	100
6.4856-7.4201	0.2444	167	0.2041	2633	X-RAY DIFFRACTION	100
7.4201-9.3339	0.2321	157	0.1859	2664	X-RAY DIFFRACTION	100
9.3339-43.967	0.2748	111	0.2572	2621	X-RAY DIFFRACTION	92

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	2.3957	-0.1118	-1.0881	1.7167	-0.2397	1.8443	-0.0975	-0.1014	-0.3922	-0.2848	0.0554	-0.1825	0.0493	0.218	-0.0001	0.9233	-0.11	0.045	0.8161	-0.005	0.8984	47.1534	29.0865	55.7835
2	0.7346	0.5408	0.9831	1.2509	0.6598	0.1175	-0.0544	0.5268	-0.8306	0.0687	0.0307	-0.2568	-0.3046	0.1066	-0.0005	0.8832	-0.1875	0.0801	1.1464	0.0805	0.9232	61.3068	41.9157	48.6983
3	0.7153	-2.1113	0.4912	1.2754	1.0016	0.4172	0.1963	-0.0541	-0.3417	0.0093	-0.045	0.2822	-0.1016	-0.0632	0.0001	0.9177	-0.1242	0.1721	1.0102	-0.0755	1.499	116.4689	87.7688	37.1461
4	0.3587	0.0519	0.1185	2.1319	0.8395	-1.198	0.1862	0.1604	-0.1628	-0.0657	-0.1524	-0.3235	-0.3746	0.0895	-0.0001	1.072	-0.3703	0.0598	1.2485	0.0717	0.8764	72.3043	59.5146	49.0605
5	2.8234	-0.8426	0.7945	1.9284	0.192	1.014	0.0918	0.2369	-0.1135	-0.2673	0.0241	0.2943	-0.0749	0.2453	0	1.2908	-0.2424	-0.1764	1.2045	-0.0362	1.178	28.486	47.5109	33.8829
6	1.5924	0.3629	-1.1213	1.2231	-0.0032	-0.7176	-0.1547	-0.2765	1.0878	-0.4516	-0.4409	1.3782	-0.1044	0.0267	-0.0028	1.2731	-0.4558	-0.3086	1.1699	0.18	1.1246	41.3135	61.6127	40.597
7	1.0849	-0.7758	0.2508	1.0333	0.3076	0.6895	-0.2121	-0.1311	0.2596	-0.0974	-0.1364	0.1301	-0.2146	0.0577	-0.0001	1.1526	-0.0069	0.2891	1.1636	-0.0988	1.328	88.4884	116.0755	53.2499
8	2.2053	0.4553	-1.0619	-0.0149	-0.3649	0.3108	-0.5218	0.245	0.4059	-0.3797	0.3889	0.657	-0.1393	0.0381	-0.0001	1.2059	-0.2493	-0.181	1.1457	0.1423	0.9728	58.9494	73.0259	40.1291

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 213 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 214 through 317 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 318 through 521 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 522 through 664 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 3 through 213 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 214 through 317 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 318 through 521 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 522 through 664 )

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