PDB-5j7r: 2.5 Angstrom Crystal Structure of Putative Lipoprotein from Clost...

ID or keywords:

Entry

Database: PDB / ID: 5j7r

Title

2.5 Angstrom Crystal Structure of Putative Lipoprotein from Clostridium perfringens

Components

Putative Lipoprotein

Keywords

MEMBRANE PROTEIN /

Putative Lipoprotein /

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

Function / homology

DI(HYDROXYETHYL)ETHER / :

Function and homology information

Biological species

Clostridium perfringens (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.5 Å

Authors

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

Citation

Journal: To Be Published
Title: 2.5 Angstrom Crystal Structure of Putative Lipoprotein from Clostridium perfringens
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Flores, K. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Apr 6, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	May 4, 2016	Group: Data collection

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5j7r.cif.gz	239.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5j7r.ent.gz	205.5 KB	Display	PDB format
PDBx/mmJSON format	5j7r.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/j7/5j7r ftp://data.pdbj.org/pub/pdb/validation_reports/j7/5j7r	HTTPS FTP

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Related structure data

Similar structure data	4i18-2 7k0x-1 2yjp-d 2o9a-d 6pe9-2 6loh-1 2zbw-d 5gmy-d 3kas-d 6n5e-3 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) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-idp04088

Similar structure data

Other databases

TargetTrack: CSGID-idp04088

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative Lipoprotein

B: Putative Lipoprotein

C: Putative Lipoprotein

D: Putative Lipoprotein

hetero molecules

72.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative Lipoprotein

C: Putative Lipoprotein

hetero molecules

A: Putative Lipoprotein

C: Putative Lipoprotein

hetero molecules

defined by author&software
72 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

A: Putative Lipoprotein

hetero molecules

A: Putative Lipoprotein

hetero molecules

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

3

B: Putative Lipoprotein

D: Putative Lipoprotein

hetero molecules

B: Putative Lipoprotein

D: Putative Lipoprotein

hetero molecules

defined by author&software
72.3 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

B: Putative Lipoprotein

hetero molecules

B: Putative Lipoprotein

hetero molecules

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

5

C: Putative Lipoprotein

D: Putative Lipoprotein

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

Unit cell

Length a, b, c (Å)	118.212, 118.212, 71.836
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	154
Space group name H-M	P3₂21

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	A	37 - 181
2	1	B	37 - 181
1	2	A	40 - 181
2	2	C	40 - 181
1	3	A	40 - 181
2	3	D	40 - 181
1	4	B	40 - 181
2	4	C	40 - 181
1	5	B	40 - 181
2	5	D	40 - 181
1	6	C	40 - 182
2	6	D	40 - 182

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Putative Lipoprotein / Mass: 17997.018 Da / Num. of mol.: 4 / Fragment: UNP residues 24-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium perfringens (bacteria) / Gene: FORC3_2834 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A0A0N9KSH4
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 81 / 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 Å³/Da / Density % sol: 38.9 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: Protein: 16.8 mg/ml, 0.1M Tris HCl (pH 8.3); Screen: JCSG+ (H11), 0.2M Magnesium chloride, 0.1M Bis-Tris pH 5.5, 25% (w/v) PEG 3350.

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 21, 2016 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.5→29.55 Å / Num. obs: 20303 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.2 % / B_iso Wilson estimate: 69.4 Å² / CC_1/2: 0.905 / R_merge(I) obs: 0.064 / R_sym value: 0.064 / Net I/σ(I): 49.7
Reflection shell	Resolution: 2.5→2.54 Å / Redundancy: 9.5 % / R_merge(I) obs: 0.618 / Mean I/σ(I) obs: 4.3 / % 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
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.5→29.55 Å / Cor.coef. F_o:F_c: 0.95 / Cor.coef. F_o:F_c free: 0.927 / SU B: 25.841 / SU ML: 0.276 / Cross valid method: THROUGHOUT / ESU R: 1.221 / ESU R Free: 0.332 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26771	1068	5.3 %	RANDOM
R_work	0.21885	-	-	-
obs	0.22126	19217	99.74 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 82.761 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.2 Å²	-0.1 Å²	0 Å²
2-	-	-0.2 Å²	0 Å²
3-	-	-	0.64 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→29.55 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4458	0	10	81	4549

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.02	4531
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	4543
X-RAY DIFFRACTION	r_angle_refined_deg	1.601	2.009	6134
X-RAY DIFFRACTION	r_angle_other_deg	1.517	3	10549
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.628	5	581
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.249	28.763	194
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	10.01	15	852
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	742
X-RAY DIFFRACTION	r_gen_planes_refined	0.022	0.021	5109
X-RAY DIFFRACTION	r_gen_planes_other	0.02	0.02	819
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	2.993	5.185	2330
X-RAY DIFFRACTION	r_mcbond_other	2.985	5.183	2329
X-RAY DIFFRACTION	r_mcangle_it	4.777	7.765	2909
X-RAY DIFFRACTION	r_mcangle_other	4.776	7.768	2910
X-RAY DIFFRACTION	r_scbond_it	3.589	5.621	2200
X-RAY DIFFRACTION	r_scbond_other	3.585	5.621	2200
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	5.701	8.255	3226
X-RAY DIFFRACTION	r_long_range_B_refined	8.598	40.61	4973
X-RAY DIFFRACTION	r_long_range_B_other	8.539	40.464	4943
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	16582	0.11
1	2	B	16582	0.11
2	1	A	15472	0.14
2	2	C	15472	0.14
3	1	A	15694	0.13
3	2	D	15694	0.13
4	1	B	15474	0.14
4	2	C	15474	0.14
5	1	B	15486	0.15
5	2	D	15486	0.15
6	1	C	15754	0.14
6	2	D	15754	0.14

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.344	94	-
R_work	0.258	1371	-
obs	-	-	98.92 %

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	1.6935	1.3423	-1.1137	1.5171	-0.2475	7.1485	-0.114	0.1861	-0.4071	-0.3714	-0.0878	-0.3624	-0.0102	-0.2348	0.2018	0.2612	0.0919	0.0932	0.1972	-0.061	0.1299	49.6861	72.4428	21.6714
2	2.7939	-1.2527	-0.2543	8.2994	4.6079	6.853	0.1508	-0.2744	0.0921	0.0144	0.0123	0.1389	-0.2739	-0.0967	-0.163	0.1173	-0.0213	0.0901	0.1722	-0.0589	0.0847	43.7954	83.7086	46.2146
3	7.3343	2.1694	0.2701	9.0548	3.1128	5.9745	0.2253	0.1803	0.125	-0.3019	0.3958	-0.7937	-0.4171	0.5405	-0.6212	0.0463	-0.0634	0.0628	0.2043	-0.0735	0.1075	55.6515	82.5189	46.5358
4	3.2097	2.8143	3.5615	7.2744	3.6042	9.4086	0.1475	-0.5871	-0.2682	0.3127	-0.0434	-0.2226	0.1194	-0.0877	-0.1041	0.0986	-0.0796	0.0341	0.2879	0.0128	0.0667	48.5145	78.414	55.1586
5	5.5209	-2.039	0.7454	5.9219	3.0729	2.7286	0.3123	-0.8507	-0.4616	0.6797	0.4007	-0.6651	0.4174	0.4545	-0.7129	0.3668	-0.1354	-0.0992	0.7124	-0.0418	0.2541	58.3594	77.9317	56.7812
6	0.9711	1.3138	-1.5233	2.2813	-3.1811	6.9739	-0.1529	-0.0503	-0.0305	0.0104	0.012	-0.2141	-0.2542	0.3077	0.1409	0.1384	0.0436	-0.0482	0.1267	-0.06	0.1314	31.0785	35.0872	12.537
7	8.3871	-0.7224	1.9798	2.1278	0.3071	1.9442	0.4531	0.1018	0.0286	0.181	-0.2661	0.1311	0.1748	-0.1449	-0.187	0.0883	-0.0302	0.0156	0.0618	0.0056	0.0466	14.4519	35.4852	-10.3659
8	8.1498	1.6287	1.3743	5.6372	1.882	4.2815	0.3195	0.3038	-0.7301	0.2878	0.0308	-0.0825	0.5545	0.2131	-0.3503	0.1246	0.0311	-0.0584	0.0404	-0.0393	0.0833	21.7592	26.5452	-12.6408
9	4.1802	1.8858	4.7049	9.0535	6.3887	7.95	0.4583	0.6127	0.0888	-0.0419	-0.4179	-0.1802	0.1236	0.207	-0.0404	0.2472	0.0741	0.0344	0.3556	0.0424	0.0102	19.8766	35.6223	-19.9032
10	5.0065	0.0293	-0.1251	3.0997	0.7976	6.9915	0.5454	1.1896	-0.4021	-0.1619	-0.1168	-0.1511	0.1122	0.5293	-0.4286	0.079	0.1386	-0.0477	0.3627	-0.121	0.0635	25.2694	28.3659	-23.8835
11	7.1824	-1.3029	5.3619	1.1343	-1.538	9.7783	0.3603	-0.686	-0.2059	-0.108	-0.1754	0.0539	-0.0781	-0.4034	-0.1849	0.0755	-0.004	-0.0406	0.1768	-0.0089	0.0615	45.3265	58.6031	32.2976
12	0.7966	-1.2048	0.3452	6.0029	5.0055	8.489	-0.2382	0.0665	-0.1329	0.0789	0.7718	-0.1664	-0.1501	0.8604	-0.5336	0.2031	-0.1505	0.0003	0.3288	-0.1823	0.2807	43.1492	47.7066	9.0998
13	4.323	-2.3857	-1.4264	7.1221	2.3092	7.715	-0.251	0.2804	-0.213	-0.4945	0.8888	-0.8614	-0.3971	1.5359	-0.6379	0.1541	-0.2549	0.1436	0.5911	-0.3674	0.3548	52.9628	53.0169	7.0702
14	6.7537	-0.497	-0.6903	6.0592	0.3153	6.2108	-0.6094	1.0187	-0.0061	-1.0991	0.6966	-0.2929	-0.8876	0.6334	-0.0872	0.4707	-0.4369	0.1263	0.512	-0.2135	0.2255	46.8066	56.7537	2.6357
15	5.8755	-8.289	-1.4532	13.4484	1.8618	0.7111	0.0708	-0.1304	-0.0948	-1.4242	0.1991	-0.3182	-0.2037	0.677	-0.2699	1.149	-0.6964	0.5346	1.4367	-0.4613	0.4131	54.4243	58.5812	-3.7709
16	3.2581	-1.2177	-4.0641	1.1247	1.6743	12.0633	-0.0023	0.0592	-0.0182	-0.1935	0.3016	-0.0749	-0.4878	0.0813	-0.2993	0.1532	-0.1288	0.0031	0.2025	-0.0874	0.1676	38.5467	46.0648	1.8861
17	4.4737	2.561	0.3801	2.1732	0.6275	3.9104	-0.1245	0.073	-1.0446	-0.0731	0.2629	-0.6866	0.3094	-0.1106	-0.1383	0.0726	0.0019	-0.0183	0.1113	-0.0872	0.3281	46.5282	54.2495	24.8935
18	6.2458	0.5919	-0.7125	0.6127	1.2455	8.6798	0.2463	0.4499	-2.1001	0.1551	0.24	-0.4708	0.8714	0.6418	-0.4863	0.2658	0.0534	-0.235	0.1175	-0.2323	0.8793	49.1543	43.1252	26.7447
19	8.7768	-1.3634	0.3709	6.16	-0.6656	3.373	0.5019	-0.4653	-1.6366	0.8098	-0.2593	0.1545	0.7935	-0.628	-0.2426	0.4035	-0.2312	-0.2052	0.1787	0.0889	0.4632	42.5262	45.2226	31.5631
20	5.5682	2.1266	-0.9655	2.9315	0.277	9.8088	0.4548	-0.2133	-1.2081	0.7222	-0.1732	-0.2643	1.0397	-0.2547	-0.2817	0.3842	-0.074	-0.194	0.0561	0.1087	0.4569	46.3971	37.9434	37.3923

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	37 - 69
2	X-RAY DIFFRACTION	2	A	70 - 97
3	X-RAY DIFFRACTION	3	A	98 - 124
4	X-RAY DIFFRACTION	4	A	125 - 148
5	X-RAY DIFFRACTION	5	A	149 - 182
6	X-RAY DIFFRACTION	6	B	36 - 69
7	X-RAY DIFFRACTION	7	B	70 - 98
8	X-RAY DIFFRACTION	8	B	99 - 124
9	X-RAY DIFFRACTION	9	B	125 - 147
10	X-RAY DIFFRACTION	10	B	148 - 184
11	X-RAY DIFFRACTION	11	C	40 - 68
12	X-RAY DIFFRACTION	12	C	69 - 97
13	X-RAY DIFFRACTION	13	C	98 - 129
14	X-RAY DIFFRACTION	14	C	130 - 156
15	X-RAY DIFFRACTION	15	C	157 - 182
16	X-RAY DIFFRACTION	16	D	40 - 68
17	X-RAY DIFFRACTION	17	D	69 - 96
18	X-RAY DIFFRACTION	18	D	97 - 129
19	X-RAY DIFFRACTION	19	D	130 - 156
20	X-RAY DIFFRACTION	20	D	157 - 182

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