PDB-3g5j: Crystal structure of N-terminal domain of putative ATP/GTP bindin...

ID or keywords:

Entry

Database: PDB / ID: 3g5j

Title

Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630

Components

Putative ATP/GTP binding protein

Keywords

NUCLEOTIDE BINDING PROTEIN / N-terminal domain of ATP/GTP binding protein / PSI / MCSG /

Structural Genomics /

Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

Function and homology information

tRNA 2-selenouridine synthase activity / tRNA wobble uridine modification
Similarity search - Function

Biological species

Clostridium difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.76 Å

Authors

Nocek, B. / Bigelow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of N-terminal domain of putative ATP/GTP binding protein from Clostridium difficile 630
Authors: Nocek, B. / Bigelow, L. / Cobb, G. / Joachimiak, A.

History

Deposition	Feb 5, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 10, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.name / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3g5j.cif.gz	69.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3g5j.ent.gz	58.7 KB	Display	PDB format
PDBx/mmJSON format	3g5j.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/g5/3g5j ftp://data.pdbj.org/pub/pdb/validation_reports/g5/3g5j	HTTPS FTP

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Related structure data

Similar structure data	5ysj-4 2mhe-d 5h8a-3 6otd-d 1tol-d 5mli-d 3iug-1 6yqz-d 5n15-3 6fnx-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: APC62643.2

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative ATP/GTP binding protein

B: Putative ATP/GTP binding protein

hetero molecules

31.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative ATP/GTP binding protein

hetero molecules

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

2

B: Putative ATP/GTP binding protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	96.489, 60.192, 79.107
Angle α, β, γ (deg.)	90.00, 108.62, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	B-381- HOH

Details

AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

#1: Protein	Putative ATP/GTP binding protein Mass: 15485.062 Da / Num. of mol.: 2 / Fragment: UNP residues 1-131 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD1325 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q18BI8
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 282 / 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: 3.51 Å³/Da / Density % sol: 65 %
Crystal grow	Temperature: 292 K / pH: 6.5 Details: 0.2 M Lithium citrate, 20% PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
Detector	Type: ADSC QUANTUM Q315r / Detector: CCD / Date: Jan 29, 2009 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.76→40 Å / Num. obs: 40514 / % possible obs: 94.5 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / R_merge(I) obs: 0.078 / Net I/σ(I): 18.5
Reflection shell	Resolution: 1.76→1.79 Å / Redundancy: 2.5 % / R_merge(I) obs: 0.415 / Mean I/σ(I) obs: 2.2 / % possible all: 59.3

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
MLPHARE		phasing
SHELXCD		phasing
SHELXE		model building
CCP4		model building
Coot		model building
ARP/wARP		model building
REFMAC	5.5.0054	refinement
HKL-3000		data reduction
HKL-3000		data scaling
CCP4		phasing
ARP	WARP	model building

Refinement

Method to determine structure:

SAD / Resolution: 1.76→40 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.954 / SU B: 4.773 / SU ML: 0.066 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.09 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.198	2042	5 %	RANDOM
R_work	0.172	-	-	-
obs	0.174	38452	94.8 %	-
all	-	40494	-	-

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: 13.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.08 Å²	0 Å²	-1.96 Å²
2-	-	3.47 Å²	0 Å²
3-	-	-	-3.65 Å²

Refinement step

Cycle: LAST / Resolution: 1.76→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2085	0	26	282	2393

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	2142
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	1452
X-RAY DIFFRACTION	r_angle_refined_deg	1.553	1.972	2874
X-RAY DIFFRACTION	r_angle_other_deg	0.934	3	3551
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.28	5	257
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.455	25.143	105
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.407	15	392
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.907	15	8
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	313
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2353
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	423
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	0.914	1.5	1276
X-RAY DIFFRACTION	r_mcbond_other	0.307	1.5	534
X-RAY DIFFRACTION	r_mcangle_it	1.638	2	2045
X-RAY DIFFRACTION	r_scbond_it	2.874	3	866
X-RAY DIFFRACTION	r_scangle_it	4.704	4.5	829
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.76→1.81 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.3	93	-
R_work	0.281	2083	-
obs	-	-	70.4 %

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	9.5394	-0.3309	2.2541	3.4439	-1.2606	6.5154	0.0205	-0.2047	0.6501	0.0574	-0.2054	-0.1475	-0.6836	0.3082	0.1849	0.1881	-0.0258	0.0524	0.1461	0.0044	0.1841	56.3022	38.3819	14.6246
2	2.3193	-0.2815	-0.8085	3.4051	1.6333	5.2303	0.1364	-0.0038	0.3065	0.0788	0.0611	-0.1063	-0.2308	0.4183	-0.1975	0.1088	0.0349	0.0368	0.1292	-0.0011	0.1491	52.4097	30.1135	20.5564
3	12.7334	-1.0278	3.2327	5.8477	1.9245	2.5425	0.1128	0.0532	-0.5987	0.1942	-0.0572	0.095	0.3635	-0.0308	-0.0556	0.2653	0.0071	0.0545	0.1324	0.0043	0.1718	50.4415	17.1348	14.9781
4	5.8084	0.1427	-0.7693	2.9251	-0.4031	2.7303	0.0891	-0.1758	-0.0207	0.2513	-0.049	-0.0469	-0.0735	0.1059	-0.0402	0.1536	0.0496	-0.0078	0.0938	0.0029	0.0834	51.943	23.596	18.793
5	7.2643	-0.4113	-1.6084	9.4167	2.2679	9.4716	-0.0489	-0.2966	-0.4591	0.0959	0.1443	0.2574	0.4026	0.2802	-0.0954	0.1141	0.0602	-0.0153	0.1653	0.0086	0.1469	39.1873	16.1341	11.317
6	1.4823	-0.7169	-0.7468	1.9731	0.7215	6.4499	-0.0596	-0.0742	0.0459	0.0096	0.0395	-0.082	0.0468	0.1293	0.0201	0.1326	0.0052	-0.0387	0.1212	-0.0332	0.122	32.5255	22.3602	4.9893
7	9.9419	1.9235	4.3173	0.39	1.0898	5.5184	0.1881	-0.2007	-0.6926	0.0878	-0.0535	-0.1235	0.7865	-0.2663	-0.1347	0.3009	-0.0084	-0.0507	0.2089	-0.0129	0.17	33.6126	23.4098	20.1592
8	5.1981	3.2661	-0.8348	3.4228	-0.7995	2.7209	0.0642	-0.0052	-0.0501	0.1019	0.0189	0.0227	0.1385	-0.0546	-0.0831	0.141	0.0345	0.0001	0.153	-0.0144	0.0887	41.7793	30.078	28.435
9	2.39	-0.5307	-2.6965	1.9051	2.7874	9.4224	0.1808	-0.2949	0.2637	0.0463	0.0743	-0.1204	-0.4233	0.5271	-0.2551	0.1263	-0.0019	0.0233	0.1382	-0.0155	0.1468	51.1449	33.5275	23.1385
10	6.4985	-3.1647	0.7831	3.3669	-0.4461	0.1092	0.2313	0.6473	-0.4145	-0.2916	-0.2509	0.3437	0.0359	0.0627	0.0196	0.173	0.0616	0.0052	0.2738	-0.0471	0.233	44.5866	28.8949	8.7407
11	3.6606	-1.6529	0.3233	5.0924	2.6519	8.6655	0.0103	-0.073	0.2109	0.0321	-0.0559	-0.1881	-0.1121	0.1256	0.0455	0.1054	0.0423	-0.008	0.1158	0.0042	0.1392	39.8331	36.6797	20.2042
12	5.3764	-1.9714	-1.7502	2.7782	1.2827	8.0839	0.13	0.4191	0.3096	-0.2075	-0.0745	0.0002	-0.4616	-0.0867	-0.0555	0.0999	0.0238	0.0341	0.1165	0.0398	0.1483	51.2352	33.0149	11.499
13	9.6171	-1.4326	-7.0681	1.737	1.2527	9.9172	0.0687	0.3019	0.3061	-0.3082	0.1519	-0.0948	-0.2137	0.1692	-0.2206	0.1634	0.0033	0.0069	0.1764	0.0041	0.1452	63.2012	29.0494	6.5573
14	1.6243	-0.6163	0.9817	1.365	-0.9465	3.3035	-0.0822	0.2168	0.2506	-0.0883	0.0021	-0.1321	-0.1244	0.2057	0.0801	0.1074	0.0258	-0.0094	0.1258	0.0082	0.1443	24.3274	49.9447	9.7042
15	5.7892	-3.8003	0.4114	7.023	-3.2759	7.1313	-0.1957	-0.3546	-0.2287	0.3972	0.2269	0.2287	-0.1525	-0.5665	-0.0312	0.1422	0.0387	0.0108	0.19	0.0129	0.1354	12.7036	43.9194	21.6551
16	2.2614	-0.4085	0.739	2.8105	-1.7927	4.961	-0.0471	-0.1987	-0.112	-0.1379	0.165	-0.0016	0.1913	-0.2171	-0.118	0.0704	0.0295	-0.0105	0.1112	-0.0144	0.1201	17.0082	41.3565	17.5421
17	5.325	-0.7857	3.3358	1.3623	1.3984	7.0587	0.019	-0.1308	0.1654	0.0343	-0.0342	0.0699	-0.1334	-0.1308	0.0153	0.1245	0.0307	0.0011	0.151	0.0399	0.0834	25.7372	37.818	34.0714
18	6.1372	3.2954	0.9802	3.0557	1.5729	4.0012	-0.0858	-0.2478	-0.1337	0.0786	0.1039	0.1473	0.2564	0.0946	-0.0181	0.1464	0.0473	-0.0019	0.1911	0.0092	0.1151	29.0113	31.6593	29.6244
19	0.2494	-0.712	-1.5177	2.164	4.5986	9.863	-0.0121	0.0031	-0.0329	0.2408	0.0085	0.043	0.538	-0.1366	0.0036	0.2636	-0.0788	-0.088	0.2506	0.0767	0.235	24.2085	29.1912	17.6015
20	3.081	-0.5215	-1.134	8.7573	-2.7454	1.4186	0.1303	0.1934	-0.1589	-0.3402	-0.136	0.2147	0.0697	-0.0667	0.0056	0.1419	0.0447	-0.0275	0.2387	-0.0593	0.1265	23.3017	33.7011	6.4216
21	3.3827	0.3755	1.2647	3.1865	1.4713	4.5858	0.0644	0.3645	-0.0153	-0.3329	-0.0474	-0.0072	0.163	0.0866	-0.017	0.1204	0.07	-0.005	0.1307	0.0192	0.1183	23.7979	42.5459	4.2473
22	10.8915	-3.4501	2.8181	3.7916	-1.4086	4.2588	-0.0553	-0.4071	0.3518	0.4205	0.052	-0.0989	-0.1247	0.0919	0.0033	0.1324	-0.0001	0.0044	0.1306	0.0047	0.1323	25.6807	46.8658	21.9276
23	2.6321	-1.066	-0.4065	3.7443	0.6999	3.5098	0.0654	0.0995	0.0638	0.0657	-0.0532	-0.0866	0.1585	-0.1247	-0.0121	0.0976	0.0286	-0.0088	0.1336	-0.006	0.1344	31.3695	38.4697	13.3612
24	6.165	-2.1664	-0.8624	4.9255	5.2118	8.9522	-0.019	0.1356	0.3962	-0.1342	-0.0289	-0.2467	-0.3756	0.4606	0.0479	0.0936	0.0086	-0.0087	0.1466	0.0251	0.1574	29.0808	48.447	14.0883
25	9.66	0.6569	6.1778	8.4258	1.0546	4.9628	-0.094	-0.9039	0.2394	0.5292	-0.085	0.044	-0.2319	-0.6328	0.179	0.1278	0.0295	-0.011	0.175	-0.049	0.1545	19.9984	54.2621	19.9872
26	4.6027	-5.8142	0.5581	14.7073	-5.7887	3.5843	0.1718	-0.139	0.5724	0.6739	-0.1422	-0.5539	-0.6466	0.1998	-0.0296	0.4866	-0.007	-0.1076	0.2563	-0.0528	0.3592	19.7481	61.3519	17.7709

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 12
2	X-RAY DIFFRACTION	2	A	13 - 21
3	X-RAY DIFFRACTION	3	A	22 - 28
4	X-RAY DIFFRACTION	4	A	29 - 39
5	X-RAY DIFFRACTION	5	A	40 - 47
6	X-RAY DIFFRACTION	6	A	48 - 67
7	X-RAY DIFFRACTION	7	A	68 - 72
8	X-RAY DIFFRACTION	8	A	73 - 84
9	X-RAY DIFFRACTION	9	A	85 - 92
10	X-RAY DIFFRACTION	10	A	93 - 101
11	X-RAY DIFFRACTION	11	A	102 - 113
12	X-RAY DIFFRACTION	12	A	114 - 123
13	X-RAY DIFFRACTION	13	A	124 - 131
14	X-RAY DIFFRACTION	14	B	2 - 21
15	X-RAY DIFFRACTION	15	B	22 - 29
16	X-RAY DIFFRACTION	16	B	30 - 42
17	X-RAY DIFFRACTION	17	B	43 - 58
18	X-RAY DIFFRACTION	18	B	59 - 67
19	X-RAY DIFFRACTION	19	B	68 - 75
20	X-RAY DIFFRACTION	20	B	76 - 83
21	X-RAY DIFFRACTION	21	B	84 - 91
22	X-RAY DIFFRACTION	22	B	92 - 98
23	X-RAY DIFFRACTION	23	B	99 - 113
24	X-RAY DIFFRACTION	24	B	114 - 120
25	X-RAY DIFFRACTION	25	B	121 - 125
26	X-RAY DIFFRACTION	26	B	126 - 130

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