PDB-2r47: Crystal structure of MTH_862 protein of unknown function from Met...

ID or keywords:

Entry

Database: PDB / ID: 2r47

Title

Crystal structure of MTH_862 protein of unknown function from Methanothermobacter thermautotrophicus

Components

Uncharacterized protein MTH_862

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC5901 / PSI-2 /

Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG

Function / homology

Uncharacterised conserved protein UCP004962 / Uncharacterized protein conserved in archaea (DUF2124) /

Response regulator /

Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein MTH_862

Function and homology information

Biological species

Methanothermobacter thermautotrophicus (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.88 Å

Authors

Osipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of MTH_862 protein of unknown function from Methanothermobacter thermautotrophicus.
Authors: Osipiuk, J. / Evdokimova, E. / Kudritska, M. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Aug 30, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 11, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r47.cif.gz	176.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2r47.ent.gz	152 KB	Display	PDB format
PDBx/mmJSON format	2r47.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/r4/2r47 ftp://data.pdbj.org/pub/pdb/validation_reports/r4/2r47	HTTPS FTP

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Related structure data

Similar structure data	5dos-d 6jil-1 5obj-d 5dr6-d 5orl-d 4zs0-d 5os3-d 5os6-d 3rwp-d 5dn3-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 - HomologyF&H Search
Other databases	TargetDB: APC5901

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein MTH_862

B: Uncharacterized protein MTH_862

C: Uncharacterized protein MTH_862

D: Uncharacterized protein MTH_862

E: Uncharacterized protein MTH_862

hetero molecules

86.9 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein MTH_862

B: Uncharacterized protein MTH_862

hetero molecules

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

2

C: Uncharacterized protein MTH_862

hetero molecules

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

3

D: Uncharacterized protein MTH_862

E: Uncharacterized protein MTH_862

hetero molecules

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

Unit cell

Length a, b, c (Å)	150.763, 208.637, 83.051
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	C-713- HOH

Details

Authors state that the biological unit assembly is a putative dimer

#1: Protein	Uncharacterized protein MTH_862 Mass: 17278.672 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea) Strain: Delta H / Gene: MTH_862 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O26950
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 499 / 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: 3.78 Å³/Da / Density % sol: 67.46 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2 M Ammonium sulfate, 0.2 M Sodium/potassium tartrate, 0.1 M Sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
Detector	Type: SBC-3 / Detector: CCD / Date: Jun 19, 2006
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 1.88→34.8 Å / Num. all: 106479 / Num. obs: 106479 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / B_iso Wilson estimate: 36.7 Å² / R_merge(I) obs: 0.081 / Χ²: 1.086 / Net I/σ(I): 9.7
Reflection shell	Resolution: 1.88→1.93 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.647 / Mean I/σ(I) obs: 2.13 / Num. unique all: 8030 / Χ²: 1.007 / % possible all: 98.5

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
REFMAC		refinement
PDB_EXTRACT	3	data extraction
SBC-Collect		data collection
HKL-2000		data reduction
SHELXD		phasing
MLPHARE		phasing
DM		phasing
SOLVE		phasing
RESOLVE		phasing
HKL-3000		phasing

Refinement

Resolution: 1.88→34.8 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.94 / SU B: 5.435 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2207	5306	5 %	RANDOM
R_work	0.1922	-	-	-
all	0.1936	106319	-	-
obs	0.1936	106319	99.4 %	-

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: 23.291 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.69 Å²	0 Å²	0 Å²
2-	-	-0.47 Å²	0 Å²
3-	-	-	1.16 Å²

Refinement step

Cycle: LAST / Resolution: 1.88→34.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5993	0	25	499	6517

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.022	6555
X-RAY DIFFRACTION	r_angle_refined_deg	1.616	1.988	8924
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.536	5	881
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.59	24.608	332
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.298	15	1173
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.701	15	45
X-RAY DIFFRACTION	r_chiral_restr	0.139	0.2	951
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5082
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	3151
X-RAY DIFFRACTION	r_nbtor_refined	0.315	0.2	4425
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.18	0.2	501
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.254	0.2	124
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.216	0.2	37
X-RAY DIFFRACTION	r_mcbond_it	0.972	1.5	4108
X-RAY DIFFRACTION	r_mcangle_it	1.48	2	6407
X-RAY DIFFRACTION	r_scbond_it	2.674	3	2749
X-RAY DIFFRACTION	r_scangle_it	4.007	4.5	2462

LS refinement shell

Resolution: 1.88→1.925 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.285	348	-
R_work	0.274	7074	-
all	-	7422	-
obs	-	7422	95.21 %

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	1.8163	-0.8521	0.6863	1.5932	0.7951	1.3049	0.0051	0.155	0.0885	-0.1566	-0.0317	-0.0585	-0.1489	-0.1524	0.0267	0.0134	-0.0101	-0.0017	0.0606	0.007	0.0043	26.5186	69.4127	14.8936
2	2.2834	0.2055	-0.9452	0.2699	-0.5257	1.1829	-0.0645	-0.046	-0.0026	0.086	0.1211	-0.0727	0.0015	0.0095	-0.0567	0.0239	-0.0012	-0.0147	0.0403	-0.0288	0.0356	38.3907	59.7091	21.2439
3	0.4634	-0.2278	0.2541	0.2492	-0.0105	0.5602	0.0172	0.0402	-0.0011	-0.0151	0.042	-0.0224	0.0291	0.0129	-0.0592	0.0432	-0.0128	0.0075	0.0132	-0.0424	0.0149	38.958	57.9517	20.2647
4	19.2517	2.7656	-13.5652	2.3862	-1.5909	9.6228	-0.9225	-0.897	0.0404	1.4913	0.5853	-2.1527	2.8163	1.7926	0.3372	0.3475	0.0628	-0.1792	0.3032	-0.1224	0.3368	47.4453	74.0302	27.7689
5	3.3872	1.4358	2.8288	2.7266	3.2747	7.5249	0.012	0.1105	0.0379	-0.3182	0.2171	-0.4088	-0.2671	0.2855	-0.2291	-0.0047	-0.0677	0.0766	0.028	-0.0597	0.0704	47.1562	69.2141	12.0768
6	2.741	-0.3119	-0.6861	0.7982	0.7516	0.7664	0.0313	-0.0689	0.0843	-0.1004	0.103	-0.1524	-0.0998	-0.1164	-0.1343	0.0647	-0.0047	0.0162	-0.0086	-0.031	0.0367	37.6027	77.2487	19.9423
7	1.5316	0.1315	-2.8227	0.1688	-0.4416	5.4542	0.025	0.0568	0.0982	0.033	0.12	-0.0718	0.0331	-0.1894	-0.145	0.0564	0.0064	-0.0018	0.0612	-0.0103	-0.0132	25.2405	72.9006	30.3715
8	4.6258	-0.6339	-1.3136	1.319	-0.0384	3.2921	-0.0694	0.0253	-0.0262	0.1629	0.0486	-0.0497	-0.3265	-0.2297	0.0208	0.0956	0.036	-0.0411	0.0065	-0.0082	-0.0199	23.2055	73.0296	40.6849
9	0.4096	0.1582	0.0264	1.1071	0.5341	1.0335	0.0077	0.0044	-0.0452	0.0274	0.0409	-0.0291	-0.045	-0.1491	-0.0487	0.0473	0.0063	-0.0368	0.0473	0.0023	0.0106	31.274	60.1821	39.8607
10	0.1792	0.1391	0.1121	0.4066	-0.256	1.126	0.0388	-0.0929	-0.0828	-0.0063	-0.0119	-0.0331	0.0749	-0.022	-0.0269	0.0351	0.0047	-0.0359	0.0279	0.0115	0.0307	31.533	51.7214	38.3753
11	8.4862	-4.8523	5.4484	10.2678	-5.634	4.3446	-0.1031	0.5182	-0.9315	-0.8844	-0.0152	0.3663	0.4635	0.6068	0.1183	0.034	-0.0804	-0.101	0.1232	0.0001	0.1464	13.6838	49.7489	35.8146
12	3.669	1.005	4.6234	4.2085	1.9742	5.9536	-0.1072	-0.3646	-0.1988	0.0449	0.2514	0.1524	-0.0872	-0.1884	-0.1442	-0.0127	-0.0101	-0.0224	0.0957	0.0713	-0.0032	21.5754	52.3114	48.9675
13	0.0572	0.03	0.0397	1.7052	-0.7819	0.4089	-0.0228	-0.0616	-0.0278	-0.0003	0.053	0.0279	-0.0221	-0.0407	-0.0302	0.0145	0.0031	-0.0202	0.118	0.0096	-0.0001	14.4704	62.0618	37.8081
14	0.0578	0.3371	-0.432	2.0667	-3.1418	7.1271	0.0355	-0.085	0.0118	0.0251	-0.0157	-0.0797	-0.2301	0.2103	-0.0198	0.0375	0.0201	-0.0001	0.0972	0.0127	-0.0036	23.2192	71.5264	28.3866
15	4.5329	0.4214	-3.5537	3.6103	-1.6292	6.0755	0.1486	-0.0227	0.3435	-0.1584	-0.0718	0.0047	-0.4188	0.0816	-0.0768	0.0123	-0.0099	-0.0529	0.0488	0.0081	-0.0282	3.3979	68.051	8.1402
16	0.9766	-0.5305	0.4262	1.5512	-0.1585	1.0669	0.0214	0.0337	-0.0849	-0.0809	-0.048	0.0115	0.0328	-0.019	0.0266	-0.0259	-0.0032	-0.0085	0.0805	-0.0175	0.0158	1.502	53.4883	9.4842
17	2.1176	-0.5374	-1.1603	0.1818	0.1565	1.0553	-0.0789	0.0268	-0.2207	0.0538	-0.0123	0.0339	0.035	-0.0221	0.0912	-0.0176	0.0046	-0.0101	0.0379	-0.0237	0.0805	3.7239	45.3388	11.7758
18	1.96	1.2286	-0.7459	2.4153	-0.2195	0.3357	0.0118	-0.1058	-0.211	0.1431	-0.106	-0.1542	-0.0055	0.1465	0.0942	-0.0055	0.0221	-0.0092	0.0674	-0.0125	0.0425	6.1117	46.1518	12.9724
19	5.3474	0.9398	3.358	3.3646	1.5	5.2063	-0.0224	0.2822	-0.0251	-0.0837	-0.0072	-0.3714	0.2223	0.4335	0.0296	-0.0765	0.0284	0.0369	0.1352	-0.0189	0.0462	19.1714	49.032	6.4684
20	0.8563	-0.0089	-0.3466	0.8456	0.5431	0.4845	-0.0551	0.069	-0.0297	-0.0489	0.0087	-0.018	-0.0758	0.0144	0.0464	-0.0086	-0.0134	-0.0074	0.12	0.009	0.0071	13.4648	60.0684	9.5829
21	1.4182	-1.1712	-2.3261	1.0677	2.5221	7.4089	-0.0533	0.1562	-0.0481	-0.0176	-0.0354	0.0209	0.0232	-0.393	0.0887	0.0107	-0.0241	0.0028	0.0861	-0.003	0.0052	1.4205	64.3936	21.4697
22	3.0702	-0.7537	-0.1292	9.6697	-3.5179	5.9853	0.3138	0.1596	0.1606	-0.3232	0.1831	0.0293	-0.5122	-0.0754	-0.4968	0.2259	-0.0087	0.0871	0.0297	-0.0743	0.0935	37.9456	96.128	24.6605
23	1.7353	0.4688	-0.3343	2.9333	1.3026	3.0364	0.0359	-0.0379	-0.1233	-0.1076	0.4928	-1.0677	-0.0508	0.4683	-0.5288	0.1645	-0.0336	0.0868	0.0984	-0.2062	0.441	51.1563	89.6579	26.0349
24	0.6321	1.1753	-0.7791	2.1853	-1.4486	0.9603	0.1087	-0.2763	-0.0246	0.0435	0.5854	-1.2337	0.071	0.5532	-0.6941	0.151	-0.0198	0.0479	0.2412	-0.3661	0.6642	55.8728	86.6549	27.6951
25	2.0251	1.6857	-0.4917	1.4126	-0.2636	2.3589	0.0195	0.003	-0.1401	-0.2439	0.2994	-1.4079	0.0188	0.5879	-0.3189	0.2122	-0.0304	0.126	0.3006	-0.4225	0.8701	62.2085	90.3094	28.5819
26	11.7095	-5.7327	-11.8239	18.3617	9.6419	12.894	0.4457	-0.6909	0.464	-0.6242	0.7616	-1.9166	-0.8255	0.6907	-1.2072	0.2446	-0.1786	0.2305	0.2687	-0.3256	0.7881	60.0798	105.5749	25.3407
27	2.5815	0.9601	0.2163	3.5137	1.5082	0.6922	-0.0761	0.1956	-0.0776	-0.4626	0.4864	-0.9632	-0.1291	0.2715	-0.4102	0.2984	-0.0964	0.2025	0.0692	-0.1867	0.3457	48.9457	102.3149	26.2297
28	2.3634	1.339	-3.1964	2.8461	-1.1852	6.8804	0.1094	0.0856	0.141	-0.0628	0.3691	-0.4476	-0.1257	-0.0964	-0.4785	0.1386	0.0144	0.0252	0.0399	-0.1081	0.181	42.72	95.9259	35.0248
29	2.1113	0.8585	-0.3334	6.7234	0.2546	3.6602	0.0259	-0.0508	0.1267	0.5335	0.3243	-0.3922	-0.2414	-0.1511	-0.3502	0.2182	0.1091	-0.1059	0.0032	-0.0817	0.0935	39.0095	91.698	49.0991
30	0.4291	-0.4078	-0.5644	2.2616	0.2836	0.7766	0.1182	0.0581	-0.1275	0.5065	0.272	-1.084	0.0528	0.2895	-0.3902	0.2716	0.1087	-0.3068	0.1884	-0.2664	0.6149	53.7517	84.7182	47.9135
31	0.0322	0.3361	-0.0092	3.6789	0.4674	1.8322	0.0625	-0.01	-0.2485	0.3759	0.3111	-1.4257	0.0603	0.6315	-0.3736	0.2733	0.1166	-0.2932	0.2643	-0.2732	0.7408	58.2518	79.0066	46.1822
32	15.5003	9.7431	16.7835	19.106	-0.1064	45.548	0.0205	1.3556	-0.8789	-0.9179	0.4803	-1.3584	1.7794	1.1823	-0.5008	0.1991	0.113	-0.2378	0.0552	-0.2473	0.4035	43.229	69.3837	39.7595
33	7.1959	-3.6453	2.701	4.2561	-0.3275	3.054	0.0556	-0.3674	-0.6971	0.9875	0.1007	-0.5171	0.2524	-0.0583	-0.1563	0.4818	0.0598	-0.3145	0.0673	-0.0627	0.4562	48.3591	72.7192	54.195
34	1.0429	0.8771	0.7726	5.9863	0.0637	0.6378	0.0318	-0.0791	-0.1102	0.705	0.1748	-0.5358	0.0736	-0.102	-0.2065	0.2156	0.0472	-0.1149	0.0401	-0.0522	0.0931	38.0328	79.3036	46.6278
35	4.9425	3.064	-5.316	16.7458	-22.8604	39.3122	0.2548	0.2062	0.1247	-0.3466	0.1419	-0.2415	-0.6644	0.3123	-0.3967	0.2835	-0.0154	0.1042	0.0055	-0.0743	0.1288	39.7872	96.4598	25.4379

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	-1 - 26	1 - 28
2	X-RAY DIFFRACTION	2	A	A	27 - 67	29 - 69
3	X-RAY DIFFRACTION	3	A	A	68 - 93	70 - 95
4	X-RAY DIFFRACTION	4	A	A	94 - 100	96 - 102
5	X-RAY DIFFRACTION	5	A	A	101 - 117	103 - 119
6	X-RAY DIFFRACTION	6	A	A	118 - 137	120 - 139
7	X-RAY DIFFRACTION	7	A	A	138 - 153	140 - 155
8	X-RAY DIFFRACTION	8	B	B	-1 - 16	1 - 18
9	X-RAY DIFFRACTION	9	B	B	17 - 48	19 - 50
10	X-RAY DIFFRACTION	10	B	B	49 - 93	51 - 95
11	X-RAY DIFFRACTION	11	B	B	94 - 106	96 - 108
12	X-RAY DIFFRACTION	12	B	B	107 - 118	109 - 120
13	X-RAY DIFFRACTION	13	B	B	119 - 137	121 - 139
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