PDB-5o4j: HcgC from Methanococcus maripaludis cocrystallized with SAH and p...

ID or keywords:

Entry

Database: PDB / ID: 5o4j

Title

HcgC from Methanococcus maripaludis cocrystallized with SAH and pyridinol

Components

HcgC

Keywords

TRANSFERASE / methyltransferases / biosynthesis / protein structures / enzyme catalysis / mutagenesis / [Fe]-hydrogenase / pyridinol / Hmd

Function / homology

FeGP cofactor biosynthesis protein, methyltransferase HcgC / FeGP cofactor biosynthesis protein, methyltransferase HcgC / 6-carboxy methyl-4-hydroxy-2-pyridinol / : / Chem-PJL / S-ADENOSYL-L-HOMOCYSTEINE / Uncharacterized protein

Function and homology information

Biological species

Methanococcus maripaludis S2 (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Wagner, T. / Bai, L. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.

Citation

Journal: Angew. Chem. Int. Ed. Engl. / Year: 2017
Title: A Water-Bridged H-Bonding Network Contributes to the Catalysis of the SAM-Dependent C-Methyltransferase HcgC.
Authors: Bai, L. / Wagner, T. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.

History

Deposition	May 29, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 19, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 9, 2017	Group: Database references / Category: citation / Item: _citation.title
Revision 1.2	Sep 6, 2017	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5o4j.cif.gz	449.1 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5o4j_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	5o4j_full_validation.pdf.gz	2 MB	Display
Data in XML	5o4j_validation.xml.gz	48.4 KB	Display
Data in CIF	5o4j_validation.cif.gz	69 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/o4/5o4j ftp://data.pdbj.org/pub/pdb/validation_reports/o4/5o4j	HTTPS FTP

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Related structure data

Related structure data	5o4hC 5o4mC 5o4nC 5d4vS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5o4n-d 5o4m-d 5o4h-d 5d5t-d 5d4u-d 5d4v-d 5ujy-2 5uj1-d 5h93-d 6k8o-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#50 - Feb 2004 Glycolytic Enzymes similarity (1)

Deposited unit

A: HcgC

B: HcgC

C: HcgC

D: HcgC

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, tetrameric form observed

Unit cell

Length a, b, c (Å)	72.740, 82.998, 96.123
Angle α, β, γ (deg.)	90.00, 108.03, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	HcgC Mass: 30942.623 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: / / Source: (gene. exp.) Methanococcus maripaludis S2 (archaea) / Tissue: / / Cell: / / Cell line: / / Gene: MMP1498 / Organ: / / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host: Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / Variant (production host): Star / References: UniProt: Q6LX54

#1: Protein

HcgC

Mass: 30942.623 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: / / Source: (gene. exp.)

Methanococcus maripaludis S2 (archaea) / Tissue: / / Cell: / / Cell line: / / Gene: MMP1498 / Organ: / / Details (production host): / / Cell (production host): / / Organ (production host): / / Production host:

Escherichia coli BL21(DE3) (bacteria) / Tissue (production host): / / Variant (production host): Star / References: UniProt: Q6LX54

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Non-polymers , 7 types, 855 molecules

#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 Mass: 354.436 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₈ / Comment: precipitant*YM
#5: Chemical	ChemComp-PJL / (3~{E})-3-[(~{E})-3-oxidanylprop-2-enoyl]iminopropanoic acid Mass: 157.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₇NO₄
#6: Chemical	ChemComp-LI / LITHIUM ION Mass: 6.941 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Li
#7: Chemical	ChemComp-9KH / 6-carboxy methyl-4-hydroxy-2-pyridinol Mass: 183.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₉NO₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 839 / 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: 2.23 Å³/Da / Density % sol: 44.94 % / Description: Thick transparent hexagonal brick
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: The drop consists of 1 ul of enzyme solution containing 5 mg/ml HcgC, 2 mM pyridinol and 2 mM SAH mixed with 1 ul of the reservoir solution : 40% v/v PEG 400, 100 mM Tris/HCl pH 8.5 and 200 mM LiSO4

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 11, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99999 Å / Relative weight: 1
Reflection	Resolution: 1.7→48.41 Å / Num. obs: 119006 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC_1/2: 0.997 / R_merge(I) obs: 0.071 / R_pim(I) all: 0.043 / Net I/σ(I): 9.5
Reflection shell	Resolution: 1.7→1.79 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.562 / Num. unique obs: 17367 / CC_1/2: 0.589 / R_pim(I) all: 0.334 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
SCALA	3.3.22	data scaling
MOLREP	11.4.06	phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5D4V

5d4v

Resolution: 1.7→45.702 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.73

	R_factor	Num. reflection	% reflection
R_free	0.1921	6063	5.1 %
R_work	0.159	-	-
obs	0.1607	118942	99.58 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 36.9 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→45.702 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8288	0	205	839	9332

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	8699
X-RAY DIFFRACTION	f_angle_d	0.837	11731
X-RAY DIFFRACTION	f_dihedral_angle_d	17.174	5356
X-RAY DIFFRACTION	f_chiral_restr	0.05	1379
X-RAY DIFFRACTION	f_plane_restr	0.004	1456

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.7193	0.2905	207	0.2846	3796	X-RAY DIFFRACTION	100
1.7193-1.7396	0.2985	182	0.2702	3757	X-RAY DIFFRACTION	100
1.7396-1.7608	0.294	205	0.2523	3759	X-RAY DIFFRACTION	100
1.7608-1.7831	0.2805	219	0.2495	3728	X-RAY DIFFRACTION	100
1.7831-1.8065	0.2485	208	0.2371	3752	X-RAY DIFFRACTION	100
1.8065-1.8313	0.261	221	0.2287	3712	X-RAY DIFFRACTION	100
1.8313-1.8574	0.2406	201	0.2175	3742	X-RAY DIFFRACTION	100
1.8574-1.8852	0.2561	219	0.2126	3769	X-RAY DIFFRACTION	100
1.8852-1.9146	0.2486	216	0.198	3740	X-RAY DIFFRACTION	100
1.9146-1.946	0.2187	200	0.1894	3762	X-RAY DIFFRACTION	100
1.946-1.9796	0.2187	222	0.1833	3768	X-RAY DIFFRACTION	100
1.9796-2.0156	0.2021	183	0.166	3801	X-RAY DIFFRACTION	100
2.0156-2.0543	0.1986	185	0.1608	3717	X-RAY DIFFRACTION	100
2.0543-2.0963	0.2096	170	0.152	3806	X-RAY DIFFRACTION	100
2.0963-2.1418	0.1805	207	0.1524	3781	X-RAY DIFFRACTION	100
2.1418-2.1917	0.1722	176	0.1494	3741	X-RAY DIFFRACTION	99
2.1917-2.2465	0.173	180	0.1496	3762	X-RAY DIFFRACTION	99
2.2465-2.3072	0.1764	200	0.1466	3736	X-RAY DIFFRACTION	99
2.3072-2.3751	0.1804	183	0.1443	3785	X-RAY DIFFRACTION	100
2.3751-2.4517	0.1714	192	0.1437	3804	X-RAY DIFFRACTION	100
2.4517-2.5394	0.1766	218	0.146	3746	X-RAY DIFFRACTION	100
2.5394-2.641	0.1938	205	0.1488	3750	X-RAY DIFFRACTION	100
2.641-2.7612	0.1965	200	0.1526	3760	X-RAY DIFFRACTION	99
2.7612-2.9068	0.1822	186	0.1585	3754	X-RAY DIFFRACTION	98
2.9068-3.0888	0.1996	228	0.1633	3734	X-RAY DIFFRACTION	99
3.0888-3.3273	0.189	196	0.1589	3774	X-RAY DIFFRACTION	99
3.3273-3.662	0.1893	204	0.153	3754	X-RAY DIFFRACTION	99
3.662-4.1916	0.1642	213	0.1345	3758	X-RAY DIFFRACTION	99
4.1916-5.2797	0.1554	219	0.1254	3768	X-RAY DIFFRACTION	99
5.2797-45.7184	0.207	218	0.171	3863	X-RAY DIFFRACTION	100

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	0.0187	0.0352	0.0043	0.0503	-0.0316	0.0197	0.0138	0.0909	0.0073	0.076	0.0285	-0.1657	0.2229	0.3447	0.0001	0.252	0.089	-0.0248	0.2741	-0.0191	0.2826	-45.4812	-55.069	192.4739
2	0.0293	0.0179	-0.0403	0.0565	-0.0119	0.0462	0.0541	-0.0478	-0.1434	-0.0002	0.0801	-0.1179	0.1868	0.0699	-0.0001	0.229	0.0173	0.0041	0.1673	-0.0186	0.2019	-63.2896	-56.8661	167.1608
3	0.1361	0.0851	0.0262	0.1829	-0.1044	0.1704	-0.1651	0.1906	-0.0086	-0.4307	0.2468	-0.2034	-0.1611	0.282	0.0441	0.3985	-0.0751	0.0512	0.2634	-0.0106	0.2398	-61.1464	-45.8978	154.9684
4	0.3363	0.153	-0.0402	0.6771	0.2846	0.1656	-0.0867	0.0467	0.075	-0.2527	0.0256	0.1782	-0.1561	-0.1146	-0.0241	0.291	0.0123	-0.0473	0.186	0.0237	0.2199	-74.5591	-45.7347	162.6781
5	0.064	0.0465	0.0375	0.2848	0.2936	0.3365	0.0268	0.0005	0.0102	0.0216	0.0174	-0.042	0.0489	0.0642	-0	0.1731	0.0179	0.0071	0.1644	0.0045	0.2003	-56.1945	-48.1084	183.4396
6	0.1894	0.186	-0.2149	0.5232	-0.0296	0.2246	0.0444	0.1089	-0.2013	-0.0474	0.092	0.1037	0.1502	-0.0616	-0.0004	0.2162	0.0227	-0.011	0.1787	0.0039	0.211	-67.2609	-59.2079	175.5367
7	0.1328	0.0268	0.1687	0.3058	0.1104	0.557	-0.1756	0.0575	0.159	0.0437	-0.0235	-0.0297	-0.4593	0.0233	-0.0236	0.2709	0.018	-0.0349	0.1583	-0.0172	0.2165	-60.0799	-32.5108	194.8096
8	0.1113	-0.0525	-0.0753	0.287	0.0286	0.3343	-0.0471	-0.0385	0.0874	0.2485	0.0589	-0.4564	-0.2751	0.3715	-0.0305	0.351	-0.032	-0.1228	0.3087	-0.0307	0.339	-39.9477	-34.9789	211.8488
9	0.2592	-0.2133	-0.2485	0.5083	0.1057	0.2915	-0.0223	-0.1309	-0.0431	0.3273	0.029	-0.124	0.0818	0.1359	-0.0107	0.358	0.0375	-0.0799	0.2659	-0.0052	0.2321	-48.8996	-47.103	214.9834
10	0.2026	0.1331	0.1139	0.5985	0.0738	0.5771	-0.0279	-0.0146	-0.0002	0.065	-0.011	0.0037	-0.1407	0.0148	0	0.2058	0.0183	0.0007	0.1753	-0.0065	0.2021	-59.7344	-39.061	193.6561
11	0.4091	0.0119	-0.2272	0.4879	0.2661	0.2734	-0.3069	-0.327	0.3115	-0.0798	0.2415	0.4185	-0.2383	-0.504	0.1894	0.0632	0.3063	0.1006	0.4586	-0.1827	0.3456	-93.3898	-47.7004	196.3718
12	0.0272	0.0649	-0.0577	0.0817	-0.1601	0.292	-0.0129	-0.0331	-0.1446	-0.0219	0.0946	0.6425	-0.2757	-0.6068	-0.0589	0.1895	0.1224	-0.0935	0.5615	-0.0696	0.5816	-106.51	-52.6426	175.6771
13	0.0396	0.0108	-0.0522	0.0149	-0.0053	0.07	-0.0719	-0.1298	0.0303	-0.0687	0.0375	0.1096	-0.0103	-0.1545	0.0026	0.1189	-0.0599	0.0099	0.6122	0.023	0.747	-108.1014	-61.6535	185.1338
14	0.0095	-0.0344	0.0351	0.3144	-0.2823	0.2852	0.2412	-0.0632	-0.0272	-0.2584	0.0946	0.3029	0.181	-0.1538	-0.0221	0.3228	-0.0573	-0.1628	0.5667	-0.0412	0.8304	-110.423	-67.5177	172.6953
15	0.3871	-0.368	-0.1204	0.4671	-0.2021	0.396	0.07	0.0961	-0.0975	-0.1777	-0.0798	0.2817	0.0807	-0.1887	0.0279	0.2009	0.0299	-0.0715	0.2737	-0.036	0.3454	-92.8535	-58.0799	171.8526
16	0.0351	-0.0457	0.0257	0.0504	0.0128	0.0274	-0.1614	-0.1841	0.0069	0.0905	-0.0058	0.196	-0.1253	-0.2758	0.0002	0.2032	0.0564	0.0388	0.275	-0.0286	0.2457	-83.3353	-51.9072	194.807
17	0.1425	-0.2235	0.1305	0.4087	-0.3737	0.3196	-0.1979	-0.2536	0.0056	0.1714	0.1682	0.2348	-0.0739	-0.387	0.0318	0.1941	0.0481	0.085	0.4163	-0.0142	0.319	-91.5322	-56.9913	200.8713
18	0.7984	0.3606	-0.065	0.5862	0.0563	0.172	-0.2482	0.1202	0.1953	-0.0465	0.2567	0.1306	-0.341	-0.2149	0.0198	0.1922	0.1721	-0.0299	0.2352	-0.0604	0.3293	-88.2618	-44.7762	185.7115
19	0.0591	-0.134	0.131	0.2213	0.0245	0.1483	0.1919	-0.2385	-0.1411	0.1491	-0.0295	0.1877	0.5575	-0.3627	0.0087	0.3157	0.0011	0.0562	0.2663	0.0253	0.2673	-77.4318	-70.8739	204.0368
20	0.6163	-0.0176	0.2045	0.072	0.0637	0.1315	0.0756	-0.4868	-0.2894	0.272	0.1089	0.1719	0.3777	-0.3598	0.0579	0.4839	0.0446	0.0853	0.4387	0.0675	0.2471	-71.9609	-70.0337	228.369
21	0.1831	-0.1487	-0.0639	0.154	0.0016	0.1283	-0.1797	-0.3549	0.0627	0.0943	0.2817	0.1933	0.0211	-0.5176	0.2879	0.2889	0.0616	0.3299	0.9615	0.0793	0.1453	-83.1481	-65.3702	232.1253
22	0.3234	0.1021	0.0828	0.1442	0.0078	0.1599	-0.1294	-0.2189	0.0729	0.1488	0.0182	-0.0017	-0.0876	-0.1178	-0.2523	0.3473	0.1044	0.0516	0.3276	-0.0338	0.185	-69.2576	-55.7451	224.7589
23	0.3446	-0.1795	0.3278	0.2992	-0.1543	0.154	0.0349	-0.1382	0.0166	0.0651	0.0458	0.1783	0.0138	-0.3578	0.0613	0.1835	0.0013	0.0763	0.3245	0.0064	0.2313	-83.2629	-63.8278	202.0517
24	0.0971	-0.1144	-0.0472	0.1837	-0.0566	0.1113	-0.0664	0.0186	-0.0402	0.032	0.0602	0.0308	-0.1319	0.0932	0	0.2698	0.0126	0.0459	0.2363	-0.0063	0.2261	-66.8286	-65.3891	206.6645

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 17 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 18 through 37 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 38 through 99 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 100 through 176 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 177 through 238 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 239 through 264 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 37 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 38 through 99 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 100 through 176 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 177 through 261 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 37 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 38 through 72 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 73 through 85 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 86 through 100 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 101 through 176 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 177 through 194 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 195 through 238 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 239 through 263 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 2 through 37 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 38 through 72 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 73 through 99 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 100 through 176 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 177 through 238 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 239 through 262 )

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