PDB-5vrv: 2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (...

ID or keywords:

Entry

Database: PDB / ID: 5vrv

Title

2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (DUF2156) of Putative Lysylphosphatidylglycerol Synthetase from Agrobacterium fabrum.

Components

Protein regulated by acid pH

Keywords

HYDROLASE /

OXIDOREDUCTASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / DUF2156

Function / homology

Function and homology information

lysyltransferase / phosphatidylglycerol lysyltransferase activity / membrane => GO:0016020 /

plasma membrane
Similarity search - Function

Biological species

Agrobacterium fabrum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.05 Å

Authors

Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.05 Angstrom Resolution Crystal Structure of C-terminal Domain (DUF2156) of Putative Lysylphosphatidylglycerol Synthetase from Agrobacterium fabrum.
Authors: Minasov, G. / Wawrzak, Z. / Skarina, T. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	May 11, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 24, 2017	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5vrv.cif.gz	744.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5vrv.ent.gz	643.3 KB	Display	PDB format
PDBx/mmJSON format	5vrv.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/vr/5vrv ftp://data.pdbj.org/pub/pdb/validation_reports/vr/5vrv	HTTPS FTP

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Related structure data

Similar structure data	5ci4-1 1jqc-d 2a27-4 7m0v-d 6b31-d 2av8-d 2yab-d 4e4q-2 7m0x-d 6nfy-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) 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-IDP91591

Similar structure data

Other databases

TargetTrack: CSGID-IDP91591

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #97 - Jan 2008 Circadian Clock Proteins similarity (1)

Deposited unit

A: Protein regulated by acid pH

B: Protein regulated by acid pH

C: Protein regulated by acid pH

D: Protein regulated by acid pH

E: Protein regulated by acid pH

F: Protein regulated by acid pH

hetero molecules

223 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein regulated by acid pH

B: Protein regulated by acid pH

hetero molecules

defined by author&software
74.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Protein regulated by acid pH

D: Protein regulated by acid pH

hetero molecules

defined by author&software
74.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Protein regulated by acid pH

F: Protein regulated by acid pH

hetero molecules

defined by author&software
74.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	194.403, 194.403, 50.228
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	Protein regulated by acid pH Mass: 37139.137 Da / Num. of mol.: 6 / Fragment: residues 540-866 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium fabrum (strain C58 / ATCC 33970) (bacteria) Strain: C58 / ATCC 33970 / Gene: lpiA, Atu2521 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 Gold / References: UniProt: A9CHP8
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 669 / 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: 2.46 Å³/Da / Density % sol: 50 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 70.0 mg/ml, 0.01M HEPES (pH 7.5), Screen: 0.2M Potassium citrate, 0.3M 3-(1-Pyridinio)-1-propanesulfonate, 20% (w/v) P3350 20%

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 20, 2017 / Details: C(111)
Radiation	Monochromator: Be / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.05→30 Å / Num. obs: 133171 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / B_iso Wilson estimate: 33.7 Å² / R_merge(I) obs: 0.084 / R_pim(I) all: 0.039 / R_sym value: 0.084 / Χ²: 1.138 / Net I/σ(I): 20.4
Reflection shell	Resolution: 2.05→2.09 Å / Redundancy: 5.1 % / R_merge(I) obs: 0.775 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6765 / CC_1/2: 0.694 / R_pim(I) all: 0.38 / R_sym value: 0.775 / Χ²: 1.002 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.05→29.65 Å / Cor.coef. F_o:F_c: 0.957 / Cor.coef. F_o:F_c free: 0.938 / SU B: 10.737 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.167 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22818	6697	5 %	RANDOM
R_work	0.18964	-	-	-
obs	0.19161	126438	99.94 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 42.957 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.53 Å²	0.27 Å²	0 Å²
2-	-	0.53 Å²	0 Å²
3-	-	-	-1.72 Å²

Refinement step

Cycle: 1 / Resolution: 2.05→29.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14802	0	29	669	15500

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	15252
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	14123
X-RAY DIFFRACTION	r_angle_refined_deg	1.429	1.963	20572
X-RAY DIFFRACTION	r_angle_other_deg	0.881	3	32566
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.288	5	1907
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	23.234	23.32	744
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.424	15	2336
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.145	15	130
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2199
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.02	17302
X-RAY DIFFRACTION	r_gen_planes_other	0.018	0.02	3416
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	1.499	3.024	7634
X-RAY DIFFRACTION	r_mcbond_other	1.498	3.024	7633
X-RAY DIFFRACTION	r_mcangle_it	2.324	4.521	9539
X-RAY DIFFRACTION	r_mcangle_other	2.324	4.521	9540
X-RAY DIFFRACTION	r_scbond_it	2.016	3.319	7618
X-RAY DIFFRACTION	r_scbond_other	2.015	3.319	7618
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.157	4.867	11034
X-RAY DIFFRACTION	r_long_range_B_refined	4.91	36.668	16974
X-RAY DIFFRACTION	r_long_range_B_other	4.858	36.522	16876
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.05→2.103 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	450	-
R_work	0.269	9391	-
obs	-	-	99.72 %

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	2.1548	0.2094	0.4701	1.6404	-0.8906	2.4776	0.0537	-0.2649	0.0011	0.2248	-0.0467	0.1107	-0.2199	0.1631	-0.007	0.0648	-0.0396	0.0114	0.1024	-0.0042	0.0119	18.9634	28.4292	26.3444
2	1.1275	0.0833	0.0625	0.8253	-0.1491	1.0602	-0.0414	0.0959	-0.1206	-0.083	0.0568	-0.0203	0.0536	0.2595	-0.0155	0.0665	-0.0437	-0.0068	0.1293	-0.0168	0.0289	26.4295	28.5511	6.6095
3	2.3171	0.2392	-0.2703	0.3903	-0.0927	1.0579	-0.0067	0.1904	-0.0001	-0.015	0.0701	0.0162	-0.1916	0.1036	-0.0634	0.0913	-0.0673	-0.0149	0.1143	0.0053	0.0183	20.9008	36.3978	4.7966
4	2.2082	-0.6753	-0.897	0.3026	0.7024	2.5586	0.0553	0.0807	-0.0286	-0.0594	0.0173	0.0035	-0.0917	0.0454	-0.0726	0.0812	-0.0543	-0.015	0.0668	0.01	0.1007	14.4364	24.2747	9.2494
5	0.9589	0.0264	0.7318	2.1396	0.3986	2.0465	-0.0709	0.1796	-0.092	-0.1715	0.0631	-0.1186	-0.1934	-0.0668	0.0078	0.1183	-0.0101	0.0069	0.1234	-0.0149	0.0293	-12.8599	30.8962	-3.9458
6	1.2088	-0.8912	-0.4597	3.0164	2.7318	3.3358	-0.0695	0.0602	-0.1949	0.0941	-0.0735	0.2113	0.1101	-0.3677	0.143	0.0456	-0.0122	0.0306	0.1474	0.0076	0.0703	-23.8803	26.2355	13.7006
7	1.4886	0.0878	-0.2391	1.0921	0.1855	1.0555	-0.0483	-0.0777	0.0189	0.0158	0.0249	0.0098	-0.2946	-0.1486	0.0234	0.1536	0.0736	-0.023	0.0658	-0.0047	0.0058	-15.2024	41.9338	18.3603
8	2.6812	0.4753	-0.6629	0.2092	-0.3512	1.6903	0.0097	-0.1564	-0.1119	0.0701	-0.0141	0.0473	-0.1611	-0.0429	0.0043	0.0744	0.0203	0.0062	0.0394	-0.0086	0.0739	-10.5551	26.1253	12.9612
9	2.5419	0.1663	0.2461	1.665	-0.609	2.4623	-0.0508	0.2258	-0.0193	-0.2414	0.0511	0.0656	0.04	0.1041	-0.0004	0.0659	-0.0441	-0.0054	0.1169	-0.0148	0.0059	34.3385	114.2982	3.9159
10	1.0609	0.231	0.5922	0.8529	-0.0674	1.2992	-0.0356	-0.0343	0.1734	-0.0296	-0.0182	0.1016	-0.3222	-0.0066	0.0538	0.1169	-0.04	0.0171	0.1323	-0.035	0.0858	37.0211	121.6776	23.751
11	1.0432	0.3784	0.294	1.5782	0.2236	1.2329	0.0191	0.0576	-0.0121	0.0158	0.0206	-0.0317	0.0188	0.1565	-0.0397	0.0182	-0.0307	0.002	0.1422	-0.0022	0.0032	43.07	111.8479	25.3481
12	0.652	0.6748	0.0827	2.2519	0.762	2.0968	0.0218	-0.0653	0.0825	0.1789	0.0233	0.0088	0.0292	-0.0146	-0.0451	0.0195	-0.0026	-0.0159	0.1293	0.0199	0.0884	28.4063	112.923	21.0438
13	2.3542	-0.0595	-0.663	2.3191	-0.0828	2.2235	0.0712	-0.2564	0.0518	0.2438	-0.0545	-0.058	0.2049	0.2525	-0.0167	0.1211	-0.0232	-0.0146	0.1175	0.0101	0.0057	20.626	84.643	34.8446
14	0.6369	0.2792	-0.4651	1.1491	0.0517	1.6284	0.0384	-0.0023	-0.0502	-0.0901	-0.0289	0.0225	0.2697	0.064	-0.0095	0.118	0.0367	-0.0274	0.0591	-0.0085	0.0097	23.0004	79.9369	14.848
15	1.618	0.0994	0.1796	2.4129	-0.2256	1.7609	-0.0178	0.0902	-0.0773	-0.1099	0.021	-0.0307	0.3367	0.2031	-0.0032	0.1585	0.0081	0.024	0.0828	-0.0321	0.0188	24.4853	78.9412	12.5988
16	1.8687	0.7861	0.3547	1.8376	0.1283	1.5503	0.0125	0.1589	0.0776	0.0032	0.0064	0.1527	0.1211	0.0207	-0.019	0.0299	-0.0119	0.0103	0.0349	-0.0001	0.0236	16.6675	90.2967	19.4608
17	2.2655	-0.159	-1.4737	3.2075	-0.1147	5.705	-0.0913	0.2625	-0.008	-0.1167	0.0094	0.0245	0.5296	0.0103	0.0819	0.123	-0.0028	-0.006	0.0465	0.0015	0.0048	83.0682	15.4934	10.9354
18	2.5154	-0.5793	-1.7037	2.5546	0.9717	2.3321	0.0664	0.2464	0.1411	-0.3138	-0.0632	0.0637	0.0817	-0.0468	-0.0032	0.0776	0.0208	0.0031	0.1069	0.0358	0.0193	87.985	27.5209	7.2717
19	1.0506	-0.1591	-0.0834	1.0837	0.0156	0.8223	-0.0548	-0.0421	-0.0318	0.1898	0.0469	-0.0563	0.3649	0.1518	0.0079	0.2022	0.0624	-0.0059	0.0666	0.0148	0.0162	84.8689	17.6985	29.4421
20	1.422	0.3819	-0.2425	1.2933	-0.2537	1.3044	0.0306	-0.0208	0.1802	-0.0341	-0.0393	-0.0691	0.2092	0.1269	0.0087	0.0478	0.0017	0.0003	0.0629	0.0036	0.0681	87.399	29.6148	23.4486
21	1.046	0.3258	0.3036	1.4271	0.4391	1.9878	0.0636	-0.1264	0.0497	0.2668	-0.0692	-0.1028	-0.0295	-0.1206	0.0056	0.0732	-0.0458	-0.0162	0.1059	-0.0108	0.0214	65.3267	50.5833	35.1402
22	2.0352	1.3998	-1.5644	5.8428	-3.2058	6.0564	-0.0145	0.1802	0.2987	-0.1839	0.2641	0.206	-0.2901	-0.4499	-0.2496	0.052	-0.0201	-0.0021	0.2022	0.0007	0.1258	46.4795	48.3117	8.6809
23	1.9237	-0.0117	0.6261	1.1411	0.0371	0.9361	0.0279	0.0174	0.0744	-0.0114	-0.0352	-0.0487	0.0166	-0.1472	0.0074	0.0171	-0.0437	0.0027	0.1499	-0.0046	0.0267	57.2534	42.7492	17.3749
24	0.8003	-1.0952	-0.1303	2.0051	-0.5207	1.7473	0.0769	0.0665	0.0984	-0.0993	-0.0132	-0.0279	0.0149	-0.0052	-0.0637	0.0719	-0.0578	-0.0094	0.1392	0.0059	0.1862	70.1062	47.9957	22.1676

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	537 - 612
2	X-RAY DIFFRACTION	2	A	613 - 686
3	X-RAY DIFFRACTION	3	A	687 - 810
4	X-RAY DIFFRACTION	4	A	811 - 865
5	X-RAY DIFFRACTION	5	B	537 - 621
6	X-RAY DIFFRACTION	6	B	622 - 662
7	X-RAY DIFFRACTION	7	B	663 - 810
8	X-RAY DIFFRACTION	8	B	811 - 863
9	X-RAY DIFFRACTION	9	C	537 - 612
10	X-RAY DIFFRACTION	10	C	613 - 682
11	X-RAY DIFFRACTION	11	C	683 - 812
12	X-RAY DIFFRACTION	12	C	813 - 864
13	X-RAY DIFFRACTION	13	D	537 - 612
14	X-RAY DIFFRACTION	14	D	614 - 714
15	X-RAY DIFFRACTION	15	D	715 - 822
16	X-RAY DIFFRACTION	16	D	823 - 863
17	X-RAY DIFFRACTION	17	E	537 - 562
18	X-RAY DIFFRACTION	18	E	563 - 611
19	X-RAY DIFFRACTION	19	E	612 - 822
20	X-RAY DIFFRACTION	20	E	823 - 865
21	X-RAY DIFFRACTION	21	F	537 - 653
22	X-RAY DIFFRACTION	22	F	654 - 685
23	X-RAY DIFFRACTION	23	F	686 - 812
24	X-RAY DIFFRACTION	24	F	813 - 864

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