PDB-6or2: MmpL3 is a lipid transporter that binds trehalose monomycolate an...

ID or keywords:

Entry

Database: PDB / ID: 6or2

Title

MmpL3 is a lipid transporter that binds trehalose monomycolate and phosphatidylethanolamine

Components

Membrane protein, MmpL family protein

Keywords

MEMBRANE PROTEIN / transporter

Function / homology

Function and homology information

D-mannose binding / defense response / toxin activity
Similarity search - Function

Biological species

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.59 Å

Authors

Su, C.-C.

Funding support

United States, 1items

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: MmpL3 is a lipid transporter that binds trehalose monomycolate and phosphatidylethanolamine.
Authors: Su, C.C. / Klenotic, P.A. / Bolla, J.R. / Purdy, G.E. / Robinson, C.V. / Yu, E.W.

History

Deposition	Apr 29, 2019	Deposition site: RCSB / Processing site: RCSB
Supersession	May 29, 2019	ID: 6N3T
Revision 1.0	May 29, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 5, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jun 12, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	Mar 13, 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

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Validation report

Summary document	6or2_validation.pdf.gz	786.8 KB	Display	wwPDB validaton report
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Data in XML	6or2_validation.xml.gz	28.2 KB	Display
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Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/or/6or2 ftp://data.pdbj.org/pub/pdb/validation_reports/or/6or2	HTTPS FTP

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Related structure data

Related structure data	6n40
Similar structure data	6n40-d 4rh6-d 4n5e-d 1z4y-2 5oni-d 4uba-d 1z4w-2 4atv-2 3zhz-d 2y1d-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	#124 - Apr 2010 Concanavalin A and Circular Permutation similarity (7) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (7)

Deposited unit

A: Membrane protein, MmpL family protein

hetero molecules

86.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	80.814, 129.457, 154.591
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Membrane protein, MmpL family protein / MmpL3 Mass: 85442.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0250 / Variant: ATCC 700084 / mc(2)155 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QP27
#2: Chemical	ChemComp-L9Q / (1S)-2-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate / 1-stearoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine Mass: 746.050 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄₁H₈₀NO₈P
#3: Sugar	ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 11 / 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: 4.73 Å³/Da / Density % sol: 74.01 %
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

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 18, 2018

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.56→100 Å / Num. obs: 51822 / % possible obs: 97.4 % / Redundancy: 4 % / R_merge(I) obs: 0.081 / R_pim(I) all: 0.045 / R_rim(I) all: 0.093 / Χ²: 0.985 / Net I/σ(I): 5.6 / Num. measured all: 206933

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.56-2.65	3.5	2.237	5018	0.11	1.31	2.614	1.012	96.3
2.65-2.76	4.1	1.89	5152	0.211	1.036	2.172	0.973	98.2
2.76-2.88	4.1	1.32	5228	0.46	0.722	1.515	0.966	99.5
2.88-3.04	4	0.812	5168	0.648	0.45	0.935	0.939	98.5
3.04-3.23	3.9	0.494	5238	0.83	0.274	0.569	0.975	98.8
3.23-3.47	4.1	0.284	5216	0.94	0.153	0.325	1.014	99.2
3.47-3.82	3.9	0.145	5169	0.983	0.08	0.167	1.045	97.3
3.82-4.38	4.2	0.08	5218	0.994	0.041	0.09	0.992	97.7
4.38-5.52	4	0.053	5164	0.997	0.028	0.061	0.959	96
5.52-100	4.1	0.036	5251	0.995	0.02	0.042	0.983	93.2

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3318: ???)	refinement
SCALEPACK		data scaling
PDB_EXTRACT	3.25	data extraction
DENZO		data reduction
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.59→99.252 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.89 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2896	3506	3.87 %
R_work	0.2492	-	-
obs	0.2507	90546	92.91 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.59→99.252 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5581	0	85	11	5677

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	5785
X-RAY DIFFRACTION	f_angle_d	0.523	7857
X-RAY DIFFRACTION	f_dihedral_angle_d	14.564	3464
X-RAY DIFFRACTION	f_chiral_restr	0.038	938
X-RAY DIFFRACTION	f_plane_restr	0.004	982

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 (%)
2.59-2.6255	0.4669	115	0.4452	2809	X-RAY DIFFRACTION	76
2.6255-2.663	0.4064	111	0.4515	2953	X-RAY DIFFRACTION	79
2.663-2.7028	0.466	131	0.4302	3282	X-RAY DIFFRACTION	88
2.7028-2.745	0.4111	132	0.4019	3359	X-RAY DIFFRACTION	89
2.745-2.79	0.3437	137	0.3821	3548	X-RAY DIFFRACTION	94
2.79-2.8381	0.4059	145	0.3831	3551	X-RAY DIFFRACTION	95
2.8381-2.8897	0.3644	141	0.3656	3602	X-RAY DIFFRACTION	95
2.8897-2.9453	0.3793	148	0.356	3564	X-RAY DIFFRACTION	96
2.9453-3.0054	0.3727	148	0.3554	3590	X-RAY DIFFRACTION	94
3.0054-3.0708	0.3579	142	0.3369	3442	X-RAY DIFFRACTION	93
3.0708-3.1422	0.3382	145	0.3227	3610	X-RAY DIFFRACTION	96
3.1422-3.2208	0.3703	148	0.3139	3643	X-RAY DIFFRACTION	97
3.2208-3.3079	0.3579	150	0.2981	3607	X-RAY DIFFRACTION	97
3.3079-3.4052	0.3029	146	0.274	3606	X-RAY DIFFRACTION	96
3.4052-3.5152	0.3169	149	0.2681	3630	X-RAY DIFFRACTION	96
3.5152-3.6408	0.3502	147	0.2511	3569	X-RAY DIFFRACTION	95
3.6408-3.7866	0.2377	135	0.2289	3435	X-RAY DIFFRACTION	92
3.7866-3.9589	0.2479	147	0.2153	3583	X-RAY DIFFRACTION	96
3.9589-4.1676	0.2464	147	0.2134	3635	X-RAY DIFFRACTION	96
4.1676-4.4288	0.2358	146	0.2001	3576	X-RAY DIFFRACTION	96
4.4288-4.7707	0.2419	140	0.1876	3524	X-RAY DIFFRACTION	94
4.7707-5.2508	0.2283	144	0.1905	3492	X-RAY DIFFRACTION	93
5.2508-6.0105	0.2767	141	0.2379	3551	X-RAY DIFFRACTION	95
6.0105-7.5722	0.2767	135	0.2481	3438	X-RAY DIFFRACTION	92
7.5722-99.3249	0.2945	136	0.2373	3441	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	1.2754	-1.0402	-0.6572	2.9095	1.8	4.533	0.0302	-0.0008	0.0573	-0.4234	-0.2859	0.1893	-0.3718	-0.575	0.3061	0.9781	0.0105	0.0217	0.7198	0.0572	0.6637	134.2214	73.662	55.2477
2	2.2657	0.5733	0.1042	1.8868	0.7467	4.3782	0.0084	0.0327	0.0251	0.3934	-0.0216	0.1568	0.81	-0.0046	0.1999	0.8491	-0.0487	0.0523	0.4125	0.0328	0.6567	139.1129	53.4394	32.0505
3	6.854	2.4974	-2.6546	3.1583	-1.2959	2.918	-0.5766	1.8924	-0.1998	-1.6781	0.9354	0.6317	0.3402	-1.4829	-0.1412	1.6891	-0.1845	-0.1775	1.176	-0.2584	0.8933	131.5956	55.2519	12.2247
4	1.1746	-0.3479	-0.6254	1.5199	0.5297	5.1589	0.3472	-0.3787	0.3631	0.0032	-0.0201	-0.5003	-1.4807	0.4836	-0.3053	0.9724	-0.1284	0.0718	0.62	0.0117	0.7601	154.4924	84.8673	51.7131
5	1.3909	1.1242	0.5217	4.2357	3.1991	6.1524	-0.1752	-0.3987	0.0361	-0.2073	0.4625	-0.7	-1.055	1.4035	-0.3056	0.5848	-0.0005	-0.0031	0.9054	0.0405	0.6017	160.4725	74.1595	51.3051
6	2.1226	-0.7247	-1.6245	1.9884	1.5515	7.8949	0.0192	0.2289	0.0129	-0.3943	-0.1152	-0.0086	-0.7906	-0.0451	0.0787	0.6625	-0.0576	-0.1179	0.5186	0.0221	0.533	147.2222	63.2642	21.3636
7	0.0306	-0.0697	0.0926	0.1587	-0.2108	0.2801	0.1581	1.0372	-1.1767	0.1803	-0.1987	-0.6933	0.9437	0.7011	-0.0021	2.6235	0.8053	0.3055	1.5734	-0.4339	1.6751	136.5644	34.8616	8.3098

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 207 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 208 through 330 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 331 through 400 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 401 through 501 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 502 through 582 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 583 through 757 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 758 through 761 )

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