PDB-2i1s: Crystal Structure of Protein of Unknown Function MM3350 from Meth...

ID or keywords:

Entry

Database: PDB / ID: 2i1s

Title

Crystal Structure of Protein of Unknown Function MM3350 from Methanosarcina mazei Go1

Components

Hypothetical protein

Keywords

STRUCTURAL GENOMICS / UNKNOWN FUNCTION / Methanosarcina mazei / MAD / PSI-2 / MCSG / Hypothetical protein / Protein Structure Initiative / Midwest Center for Structural Genomics

Function / homology

MM3350-like / Plasmid pRiA4b, Orf3 / MM3350-like superfamily / Plasmid pRiA4b ORF-3-like protein / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Roll / Alpha Beta / Plasmid pRiA4b Orf3-like domain-containing protein

Function and homology information

Biological species

Methanosarcina mazei (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Nocek, B. / Borovilos, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of hypothetical protein MM_3350 from Methanosarcina mazei Go1
Authors: Nocek, B. / Borovilos, M. / Clancy, S. / Joachimiak, A.

History

Deposition	Aug 14, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 12, 2006	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2008	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3	Feb 21, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

Remark 300

BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	2i1s_validation.pdf.gz	430.7 KB	Display	wwPDB validaton report
Full document	2i1s_full_validation.pdf.gz	439 KB	Display
Data in XML	2i1s_validation.xml.gz	17.3 KB	Display
Data in CIF	2i1s_validation.cif.gz	24.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i1/2i1s ftp://data.pdbj.org/pub/pdb/validation_reports/i1/2i1s	HTTPS FTP

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Related structure data

Similar structure data	6od5-2 6s0p-d 2d5v-2 2pk8-1 6epa-d 2d5v-1 2hyj-d 3up9-d 5xgr-3 6od4-1 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: apc86124

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Hypothetical protein

B: Hypothetical protein

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

1

A: Hypothetical protein

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

2

B: Hypothetical protein

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

Unit cell

Length a, b, c (Å)	62.421, 90.577, 107.978
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 4

Dom-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	THR	THR	A	A	4 - 188	4 - 188
2	LYS	LYS	B	B	2 - 188	2 - 188

#1: Protein	Hypothetical protein Mass: 21956.713 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: MM_3350 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PRU3
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Hypothetical protein

Mass: 21956.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Methanosarcina mazei (archaea) / Strain: Go1 / Gene: MM_3350 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8PRU3

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 157 / 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: 3.47 Å³/Da / Density % sol: 64.6 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M Sodium citrate 20% isopropanol 20% PEG 4000 , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-ID / Wavelength: 0.97936, 0.97953

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2006

Radiation

Monochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97936	1
2	0.97953	1

Reflection

Resolution: 2.3→40 Å / Num. all: 26240 / Num. obs: 26070 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / R_merge(I) obs: 0.095 / Net I/σ(I): 19.2

Reflection shell

Resolution: 2.3→2.34 Å / R_merge(I) obs: 0.416 / % possible all: 59.7

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
SBC-Collect		data collection
HKL-2000		data reduction
HKL-2000		data scaling
HKL-3000		phasing
SHELXE		model building
SOLVE		phasing
RESOLVE		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MAD / Resolution: 2.3→40 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.928 / SU B: 11.217 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.232 / ESU R Free: 0.206 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24284	1328	5.1 %	RANDOM
R_work	0.192	-	-	-
all	0.1946	26070	-	-
obs	0.19456	24692	93.39 %	-

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: 41.639 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.75 Å²	0 Å²	0 Å²
2-	-	0.97 Å²	0 Å²
3-	-	-	-1.72 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2964	0	0	157	3121

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.022	3032
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.613	1.961	4100
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.687	5	358
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.61	24.967	151
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.584	15	534
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.915	15	10
X-RAY DIFFRACTION	r_chiral_restr	0.11	0.2	427
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	2314
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	1207
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.309	0.2	1999
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.255	0.2	179
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	0.172	0.2	30
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.249	0.2	7
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	0.784	1.5	1855
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.263	2	2901
X-RAY DIFFRACTION	r_scbond_it	1.988	3	1377
X-RAY DIFFRACTION	r_scangle_it	2.936	4.5	1199
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1427 / Refine-ID: X-RAY DIFFRACTION

Type	Rms dev position (Å)	Weight position
medium positional	0.37	0.5
medium thermal	1.25	2

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.295	49	-
R_work	0.23	1163	-
obs	-	-	60.48 %

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	2.424	-0.664	-1.8271	1.4497	2.2541	3.8027	0.0264	-0.1441	-0.1759	0.1206	-0.0397	0.1185	-0.2239	0.1255	0.0133	0.1972	-0.0254	0.0268	0.024	0.0494	-0.0265	13.8329	0.0987	26.0877
2	2.5568	-1.1255	2.6679	3.7335	1.0984	4.3789	-0.1415	-0.1206	0.2118	0.3317	0.021	0.272	-0.6617	-0.1591	0.1205	0.1527	-0.0135	0.0405	0.0737	0.0349	0.0445	3.7158	12.3465	21.4039
3	2.9785	1.1487	-0.0164	4.8762	-0.8875	7.5449	0.039	0.1328	-0.0906	-0.2343	-0.0607	0.1914	-0.0609	-0.0303	0.0217	0.0993	-0.0207	0.0209	-0.0241	0.026	-0.0272	8.899	5.0391	13.0797
4	1.4535	2.0972	-1.023	14.9489	10.2477	13.0329	-0.2669	0.3018	-0.1879	-0.0716	-0.2945	1.8321	0.5307	-1.1955	0.5614	-0.0144	-0.2586	0.0932	0.3976	0.0245	0.4347	-9.8641	-0.708	21.7918
5	39.258	-5.6725	-10.8974	31.321	-6.989	5.4292	0.5654	2.9061	-0.2226	-5.3828	-0.4869	2.0553	1.7514	-3.2128	-0.0785	0.7153	-0.066	-0.3075	0.3266	0.0619	0.3875	-5.8197	4.7034	8.3222
6	7.8581	-1.5691	2.6992	8.752	-2.7069	9.7201	0.0091	-0.5959	0.389	0.7236	0.3414	1.0289	-0.5516	-1.4	-0.3504	0.0456	-0.0262	0.128	0.1583	-0.0102	0.1484	-5.7464	7.7057	23.5179
7	3.5248	-1.8188	-3.0414	1.7942	3.3057	6.1475	-0.1062	0.1437	-0.3812	-0.0414	-0.3828	0.5283	0.6012	-0.2637	0.489	0.1405	-0.1176	0.0055	0.1033	0.0323	0.0259	6.5234	-0.594	15.3894
8	3.2699	-1.7138	0.0966	4.8092	3.4474	7.1544	-0.0122	-0.4726	0.0239	0.465	-0.2011	0.4164	0.0615	-0.5585	0.2133	0.1627	-0.064	0.1377	0.0552	-0.0199	0.0193	4.7851	7.0514	28.0075
9	5.5449	-1.8132	0.2914	4.5951	0.3845	2.1194	0.122	-0.2511	0.6471	0.5094	-0.2886	-0.0176	-0.508	0.346	0.1666	0.3387	-0.107	0.0263	-0.0229	-0.0088	-0.0059	12.4906	14.5319	28.1126
10	4.9505	-2.434	0.6537	3.9447	-6.6965	14.8759	-0.2073	-0.0013	-0.1181	-0.3284	0.3733	0.2056	0.7082	-0.2579	-0.1659	0.1217	-0.0499	0.0066	0.1291	0.0648	-0.0809	18.5084	-3.4698	14.5961
11	32.0811	-0.8409	-2.9583	4.8582	-5.5732	22.0784	0.0147	-1.4604	-0.817	0.0555	-0.4519	-0.0456	1.2472	0.7597	0.4373	0.1378	0.08	-0.0346	0.0643	0.1157	-0.1551	27.3231	-7.4423	18.5918
12	83.3456	-35.2249	24.4508	30.2266	6.6629	38.2435	0.9698	0.0674	-2.9348	1.0724	-0.3438	-0.4249	2.7493	2.4382	-0.626	0.0666	0.1511	0.1443	0.1117	0.1967	-0.0487	35.7151	-10.393	14.5088
13	13.5522	-8.5809	-2.6832	18.0062	-5.8	10.4038	0.2777	-0.2714	-0.0471	0.0757	-0.2596	-0.3942	0.2461	1.5703	-0.0181	-0.0186	0.0737	0.0249	0.1291	0.0603	-0.2006	31.4014	-1.1167	11.505
14	8.7584	-6.5933	-0.851	5.0284	0.1226	4.215	0.1215	0.1195	0.6916	-0.4686	0.0967	-0.1893	-0.055	0.4734	-0.2182	0.0992	-0.1298	-0.0145	0.0287	0.0492	0.0071	22.1547	10.2381	22.9475
15	31.9709	2.0811	-6.7182	21.1305	-0.2804	1.4129	-0.1552	2.1073	-0.4265	-1.0436	0.2109	0.3473	-0.1602	0.8524	-0.0557	-0.1357	-0.0551	-0.0338	0.123	0.02	-0.1231	38.8551	17.9824	-0.6302
16	33.1111	4.3917	-4.3837	2.8181	2.0607	3.7031	0.3046	-0.9768	-1.1998	1.3497	-0.4009	-0.1446	-0.0808	-0.0378	0.0963	0.0076	-0.0358	-0.0247	-0.0261	0.0407	-0.014	29.0032	13.8184	5.2502
17	0.9956	-1.2968	1.416	2.5134	-0.6581	3.7215	0.0905	-0.3228	-0.0303	-0.0152	0.1474	0.2998	0.3957	-0.1737	-0.2379	0.1009	-0.1008	0.0104	0.2277	0.0306	-0.0484	14.8007	2.457	-1.0677
18	1.2894	-0.8231	-0.789	0.5255	0.5037	0.4828	-0.0987	0.0716	-0.2051	0.4351	0.0684	-0.3502	0.4115	0.0239	0.0303	0.1305	-0.0755	-0.0462	0.1932	0.0208	-0.0423	24.4917	4.757	1.0758
19	1.4579	-0.3522	0.5881	0.3859	-0.1901	1.6325	-0.0557	-0.0549	0.0429	0.0118	-0.0859	-0.0089	0.2646	0.2527	0.1416	0.0602	-0.035	0.0253	0.1244	-0.0004	-0.0549	27.7437	11.9405	-7.5568
20	3.0949	2.2425	-1.608	5.3932	1.2252	2.6952	-0.1201	0.1641	-0.0585	-0.475	0.0388	0.1303	0.1211	0.1371	0.0813	0.0685	-0.0671	0.0039	0.0793	-0.0199	-0.0783	20.749	6.6117	-14.1782
21	7.6366	-6.8284	-1.498	7.1625	1.2869	0.2965	0.2272	-0.1293	0.186	-0.5609	0.0789	-0.2158	-0.1542	-0.4266	-0.3061	-0.0512	0.0235	0.0312	0.0103	-0.0178	-0.024	15.4348	24.3014	-5.4574
22	67.081	-7.7198	-20.5812	2.9887	8.1094	22.0063	-0.6821	5.7769	4.9912	-1.2222	-1.072	0.148	-2.2852	-0.596	1.7541	0.5676	-0.0334	-0.1447	0.3167	0.2169	0.1672	19.9192	21.344	-20.1222
23	7.3816	-0.7365	-4.0258	4.3931	-1.9683	20.219	-0.044	-0.4154	0.6881	-0.1298	0.1572	-0.0508	-0.4933	0.5126	-0.1132	-0.063	-0.0324	-0.0359	-0.0928	-0.0411	-0.1117	21.9584	20.9819	-4.6973
24	1.9181	0.5808	2.5324	1.9663	2.2166	5.3405	-0.2729	-0.0027	0.2637	-0.0665	-0.1005	0.2397	0.3631	-0.2117	0.3734	0.0838	-0.0857	-0.0045	0.0847	-0.0129	-0.0654	15.3551	8.0518	-8.8833
25	24.7507	5.4576	1.8643	4.2228	3.072	2.4855	0.6245	-1.1641	-0.7628	0.5681	-0.6113	-0.3443	0.329	-0.5658	-0.0132	-0.0376	-0.0201	-0.0392	0.1491	0.0596	-0.1825	31.0468	12.9994	8.0829
26	3.0052	3.9985	1.8005	7.7973	2.238	2.0518	-0.0057	0.04	-0.4801	0.2528	0.0672	-0.5364	0.5628	0.0399	-0.0615	0.1033	0.0227	-0.0079	0.0491	0.0194	-0.067	29.6282	2.667	0.5277
27	8.1951	8.6446	-2.3543	9.4155	-0.6347	12.1904	-0.0085	0.3307	0.0654	-0.3755	-0.0981	0.0952	0.3226	-0.7144	0.1067	0.3251	-0.1776	-0.0149	-0.0313	-0.014	-0.1146	12.1448	-3.1737	-13.0294
28	12.4653	3.4611	-6.3851	12.7993	4.1855	13.6733	-0.6455	-0.1734	0.2327	0.593	0.061	0.9675	1.3837	-0.4075	0.5845	0.4749	-0.2163	-0.073	0.1287	0.1105	-0.026	9.3566	-11.8491	-9.9702
29	14.9369	11.3522	0.8109	11.838	2.202	5.3664	-0.3671	0.1833	-1.1846	-0.3176	0.4089	-1.0412	0.787	0.0833	-0.0418	0.2154	0.0664	0.1231	-0.0301	-0.0078	-0.0537	26.0211	-6.727	-3.6248

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	12 - 24	12 - 24
2	X-RAY DIFFRACTION	2	A	A	25 - 43	25 - 43
3	X-RAY DIFFRACTION	3	A	A	44 - 56	44 - 56
4	X-RAY DIFFRACTION	4	A	A	57 - 67	57 - 67
5	X-RAY DIFFRACTION	5	A	A	68 - 83	68 - 83
6	X-RAY DIFFRACTION	6	A	A	84 - 99	84 - 99
7	X-RAY DIFFRACTION	7	A	A	100 - 109	100 - 109
8	X-RAY DIFFRACTION	8	A	A	110 - 124	110 - 124
9	X-RAY DIFFRACTION	9	A	A	125 - 139	125 - 139
10	X-RAY DIFFRACTION	10	A	A	140 - 150	140 - 150
11	X-RAY DIFFRACTION	11	A	A	151 - 158	151 - 158
12	X-RAY DIFFRACTION	12	A	A	159 - 164	159 - 164
13	X-RAY DIFFRACTION	13	A	A	165 - 174	165 - 174
14	X-RAY DIFFRACTION	14	A	A	175 - 188	175 - 188
15	X-RAY DIFFRACTION	15	B	B	2 - 6	2 - 6
16	X-RAY DIFFRACTION	16	B	B	7 - 10	7 - 10
17	X-RAY DIFFRACTION	17	B	B	11 - 21	11 - 21
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