PDB-5eum: 1.8 Angstrom Crystal Structure of ATP-binding Component of Fused ...

ID or keywords:

Entry

Database: PDB / ID: 5eum

Title

1.8 Angstrom Crystal Structure of ATP-binding Component of Fused Lipid Transporter Subunits of ABC superfamily from Haemophilus influenzae.

Components

Lipid A export ATP-binding/permease protein MsbA

Keywords

HYDROLASE / ATP-binding domain / ABC transporter superfamily / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

ABC-type lipid A-core oligosaccharide transporter / ATPase-coupled lipid transmembrane transporter activity / membrane => GO:0016020 / ATP binding / plasma membrane
Similarity search - Function

Biological species

Haemophilus influenzae PittII (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.8 Angstrom Crystal Structure of ATP-binding Component of Fused Lipid Transporter Subunits of ABC superfamily from Haemophilus influenzae.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F.

History

Deposition	Nov 18, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 2, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5eum.cif.gz	231.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5eum.ent.gz	187.7 KB	Display	PDB format
PDBx/mmJSON format	5eum.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eu/5eum ftp://data.pdbj.org/pub/pdb/validation_reports/eu/5eum	HTTPS FTP

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Related structure data

Related structure data	2ghiS S: Starting model for refinement
Similar structure data	4c2p-d 2ixf-1 4c2q-d 4gxq-1 4c2o-d 6m7f-1 5dvl-1 3mg9-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-idp91076

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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: Lipid A export ATP-binding/permease protein MsbA

B: Lipid A export ATP-binding/permease protein MsbA

hetero molecules

58.5 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)	95.237, 95.237, 60.870
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	76
Space group name H-M	P4₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Lipid A export ATP-binding/permease protein MsbA Mass: 28282.645 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus influenzae PittII (bacteria) Gene: msbA, CGSHiII_09046 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0E1SLC7, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

#1: Protein

Lipid A export ATP-binding/permease protein MsbA

Mass: 28282.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Haemophilus influenzae PittII (bacteria)
Gene: msbA, CGSHiII_09046 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0E1SLC7, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Non-polymers , 6 types, 326 molecules

#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MLI / MALONATE ION Mass: 102.046 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₂O₄
#5: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₄
#6: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.5 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 8.5 mg/ml, 0.01M Tris-HCL (pH 8.3); Screen: JCSG+ (E2), 0.2M Sodium chloride, 0.1M Sodium cacodylate (pH 6.5), 2M Ammonium sulfate; Cryo: 1:1 (screen solution) : (50% Sucrose).

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.98756 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2015
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98756 Å / Relative weight: 1
Reflection	Resolution: 1.8→30 Å / Num. obs: 50720 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / B_iso Wilson estimate: 35.2 Å² / R_merge(I) obs: 0.048 / R_sym value: 0.048 / Net I/σ(I): 32.8
Reflection shell	Resolution: 1.8→1.83 Å / Redundancy: 7.5 % / R_merge(I) obs: 0.64 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
BALBES		phasing
BLU-MAX		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2GHI

2ghi

Resolution: 1.8→29.46 Å / Cor.coef. F_o:F_c: 0.967 / Cor.coef. F_o:F_c free: 0.951 / SU B: 4.536 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20394	2598	5.1 %	RANDOM
R_work	0.17104	-	-	-
obs	0.1727	47918	99.73 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 42.179 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.45 Å²	0 Å²	0 Å²
2-	-	-0.45 Å²	0 Å²
3-	-	-	0.91 Å²

Refinement step

Cycle: 1 / Resolution: 1.8→29.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3871	0	117	305	4293

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	4366
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4134
X-RAY DIFFRACTION	r_angle_refined_deg	1.405	1.981	5922
X-RAY DIFFRACTION	r_angle_other_deg	0.85	3	9508
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.162	5	560
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.33	25.07	215
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.72	15	756
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.27	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	660
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.02	5178
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	992
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.639	2.539	2175
X-RAY DIFFRACTION	r_mcbond_other	1.626	2.531	2170
X-RAY DIFFRACTION	r_mcangle_it	2.524	3.778	2754
X-RAY DIFFRACTION	r_mcangle_other	2.524	3.778	2755
X-RAY DIFFRACTION	r_scbond_it	2.366	3.088	2191
X-RAY DIFFRACTION	r_scbond_other	2.366	3.083	2189
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.686	4.479	3168
X-RAY DIFFRACTION	r_long_range_B_refined	7.527	21.522	4867
X-RAY DIFFRACTION	r_long_range_B_other	7.455	20.904	4739
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.8→1.847 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.253	203	-
R_work	0.223	3516	-
obs	-	-	100 %

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	6.8852	0.9782	0.5424	1.6869	-0.6425	1.8693	-0.0419	0.2462	-0.0847	0.0871	0.0732	-0.2879	-0.0731	0.1606	-0.0313	0.0179	0.0001	-0.0161	0.0646	-0.074	0.1261	-13.5804	52.1095	-3.1169
2	1.7647	-1.8128	-1.9546	5.2468	1.3199	6.4741	0.2312	0.2259	0.2066	-0.3954	-0.0508	-0.2997	-0.0957	-0.1455	-0.1804	0.049	0.0192	0.037	0.0541	0.019	0.03	-27.5019	52.7703	-19.4729
3	1.5151	0.0472	0.5503	1.1904	0.3044	1.2016	0.077	0.1712	0.0618	-0.0687	0.0646	-0.2337	-0.008	0.1812	-0.1416	0.0451	0.0046	0.0137	0.0957	-0.0524	0.0827	-22.6328	48.5727	-8.1338
4	4.9754	-1.727	-0.1976	4.8904	3.1793	2.268	-0.007	-0.1557	0.3801	-0.3686	-0.1169	0.0234	-0.2714	-0.1573	0.1238	0.1145	0.0636	-0.0063	0.2004	-0.072	0.057	-10.9556	26.9207	-6.9765
5	5.4643	-1.3215	-0.7843	5.2806	-0.2368	3.1637	-0.0093	-0.2713	0.037	0.3887	-0.0341	-0.1898	0.2414	-0.1881	0.0434	0.1011	0.0076	-0.0442	0.2246	-0.0756	0.0456	-10.2542	24.7282	4.7954
6	0.1043	-0.4445	-0.4513	2.0954	2.4015	3.2289	-0.0158	-0.0013	0.0263	0.0748	-0.2787	0.0497	0.2952	-0.6612	0.2945	0.3145	-0.0238	0.0166	0.559	-0.0763	0.2844	-14.3446	23.4394	-3.8404
7	5.3234	0.2516	0.8302	5.2572	-0.7229	1.592	0.2394	-0.5064	-0.5879	0.0165	-0.1368	0.0229	0.104	-0.2027	-0.1027	0.044	0.0027	-0.0689	0.1036	0.004	0.1341	-23.8986	32.5154	1.2519
8	2.3778	0.6277	0.585	1.6304	0.7505	0.8187	0.1434	-0.1586	-0.0792	0.0762	-0.0005	0.0112	0.144	-0.1331	-0.143	0.1448	-0.0062	-0.0338	0.1302	-0.0182	0.0882	-38.2063	40.8328	-3.0894
9	1.0275	1.3048	0.5635	7.2698	-0.0938	2.2362	0.0674	0.0952	0.2661	0.2511	-0.1231	0.0203	-0.1576	0.0409	0.0557	0.0607	-0.0082	0.0623	0.0289	0.0274	0.1456	4.5443	34.9612	-27.3963
10	3.4107	-0.8175	-1.4134	1.4007	0.8074	8.8113	-0.0649	-0.3623	0.2407	0.1875	0.1715	-0.14	0.1348	0.2751	-0.1066	0.0468	0.0154	-0.0098	0.0463	-0.0323	0.0247	5.0792	20.1587	-11.7678
11	1.1592	0.0815	-0.2354	1.6242	-0.5208	1.2007	0.0729	-0.0756	0.238	0.1759	0.0734	-0.0535	-0.1908	0.0155	-0.1463	0.1	0.0041	0.0561	0.0552	-0.0142	0.0854	0.8033	24.9957	-21.9422
12	3.4282	-0.8763	-3.0187	5.6669	-1.3185	6.4934	-0.0348	-0.2684	0.1586	-0.1713	-0.1247	-0.4505	0.513	0.5412	0.1595	0.1685	0.0725	0.0396	0.0867	0.0081	0.0472	-20.8916	37.1039	-23.1524
13	5.0528	-0.6931	0.7954	5.0293	1.3834	2.788	-0.1072	0.4156	0.1652	-0.2959	0.0652	0.0802	0.2137	-0.2223	0.042	0.2645	-0.0054	0.0663	0.1473	0.0624	0.0579	-24.0604	36.9942	-35.5255
14	2.3852	-0.7986	-2.458	0.3751	0.5202	3.4128	-0.2711	0.0935	0.0111	-0.0672	0.0039	-0.1008	0.6719	-0.2617	0.2672	0.4075	-0.0133	0.0635	0.1739	-0.0076	0.148	-24.1741	33.2757	-26.2338
15	4.7506	-0.1714	1.0393	5.0045	-0.292	1.8727	-0.159	0.0276	-0.0131	-0.5237	0.2251	0.6122	0.2566	-0.1223	-0.0661	0.1454	-0.0052	-0.0106	0.0659	0.0774	0.1651	-15.0566	23.7691	-31.3199
16	1.6264	0.669	-0.8121	2.46	-0.4921	0.8738	-0.003	0.0717	-0.0092	-0.15	0.1454	0.0791	0.134	-0.1488	-0.1425	0.1328	-0.0063	0.0147	0.1448	0.0353	0.0875	-6.7847	9.4151	-26.9964

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	333 - 349
2	X-RAY DIFFRACTION	2	A	350 - 361
3	X-RAY DIFFRACTION	3	A	362 - 427
4	X-RAY DIFFRACTION	4	A	428 - 444
5	X-RAY DIFFRACTION	5	A	445 - 473
6	X-RAY DIFFRACTION	6	A	474 - 501
7	X-RAY DIFFRACTION	7	A	502 - 534
8	X-RAY DIFFRACTION	8	A	535 - 587
9	X-RAY DIFFRACTION	9	B	333 - 348
10	X-RAY DIFFRACTION	10	B	349 - 361
11	X-RAY DIFFRACTION	11	B	362 - 428
12	X-RAY DIFFRACTION	12	B	429 - 444
13	X-RAY DIFFRACTION	13	B	448 - 473
14	X-RAY DIFFRACTION	14	B	474 - 501
15	X-RAY DIFFRACTION	15	B	502 - 534
16	X-RAY DIFFRACTION	16	B	535 - 587

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