PDB-5d4u: SAM-bound HcgC from Methanocaldococcus jannaschii

ID or keywords:

Entry

Database: PDB / ID: 5d4u

Title

SAM-bound HcgC from Methanocaldococcus jannaschii

Components

Uncharacterized protein MJ0489

Keywords

UNKNOWN FUNCTION / Rossmann-like fold

Function / homology

FeGP cofactor biosynthesis protein, methyltransferase HcgC / FeGP cofactor biosynthesis protein, methyltransferase HcgC /

S-ADENOSYLMETHIONINE / Uncharacterized protein MJ0489

Function and homology information

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Fujishiro, T. / Ermler, U. / Shima, S.

Funding support

Japan,

Germany, 2items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Identification of HcgC as a SAM-Dependent Pyridinol Methyltransferase in [Fe]-Hydrogenase Cofactor Biosynthesis.
Authors: Fujishiro, T. / Bai, L. / Xu, T. / Xie, X. / Schick, M. / Kahnt, J. / Rother, M. / Hu, X. / Ermler, U. / Shima, S.

History

Deposition	Aug 9, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jul 20, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2016	Group: Database references
Revision 1.2	Jan 10, 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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Download

PDBx/mmCIF format	5d4u.cif.gz	434.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5d4u.ent.gz	357 KB	Display	PDB format
PDBx/mmJSON format	5d4u.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/d4/5d4u ftp://data.pdbj.org/pub/pdb/validation_reports/d4/5d4u	HTTPS FTP

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Related structure data

Related structure data	5d4tSC 5d4vC 5d5oC 5d5tC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5d4v-1 5d4v-2 4j30-1 5d5o-3 1zxe-1 2ho4-d 5d5o-4 3th1-2 3dzb-d 5zkp-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 - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#139 - Jul 2011 DNA Methyltransferase similarity (1)

Deposited unit

A: Uncharacterized protein MJ0489

B: Uncharacterized protein MJ0489

C: Uncharacterized protein MJ0489

D: Uncharacterized protein MJ0489

hetero molecules

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

1

A: Uncharacterized protein MJ0489

C: Uncharacterized protein MJ0489

hetero molecules

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

2

B: Uncharacterized protein MJ0489

D: Uncharacterized protein MJ0489

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.290, 70.520, 91.230
Angle α, β, γ (deg.)	90.000, 105.210, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	chain A and segid A
2	1	chain B and segid B
3	1	chain C and segid C
4	1	chain D and segid D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details	Auth asym-ID
1	1	1	chain A and segid A	A
2	1	1	chain B and segid B	B
3	1	1	chain C and segid C	C
4	1	1	chain D and segid D	D

#1: Protein	Uncharacterized protein MJ0489 / HcgC Mass: 30566.113 Da / Num. of mol.: 4 / Fragment: Rossmann-like domain, residues 1-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0489 / Plasmid: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57913
#2: Chemical	ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine Mass: 398.437 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₅H₂₂N₆O₅S
#3: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 438 / 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: 2.19 Å³/Da / Density % sol: 43.86 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2% (w/v) PEG8000, 0.5 M lithium sulfate

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2014

Radiation

Monochromator: A double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2→50 Å / Num. obs: 71397 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 2.7 % / B_iso Wilson estimate: 28.5 Å² / R_merge F obs: 0.997 / R_merge(I) obs: 0.098 / R_rim(I) all: 0.113 / Χ²: 0.965 / Net I/σ(I): 12.66 / Num. measured all: 280088

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Highest resolution (Å)	Redundancy (%)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2-2.1		2.7	0.792	0.782	2.26	36589	9737	9655	0.912	99.2
2.1-2.2			0.874	0.604	3.37	31879	7991	7961	0.696	99.6
2.2-2.3			0.909	0.466	4.59	25752	6669	6647	0.54	99.7
2.3-2.5			0.956	0.319	6.68	41151	10388	10368	0.367	99.8
2.5-2.7			0.978	0.223	9.03	30588	7570	7553	0.256	99.8
2.7-3			0.988	0.141	12.36	30416	7861	7840	0.163	99.7
3-3.3			0.993	0.091	17.55	21556	5291	5283	0.104	99.8
3.3-3.5			0.996	0.061	22.28	10301	2592	2583	0.071	99.7
3.5-3.8			0.996	0.047	25.55	10833	2930	2918	0.055	99.6
3.8-4			0.998	0.041	29.28	5927	1498	1491	0.047	99.5
4-4.3			0.997	0.037	32.76	7141	1772	1765	0.042	99.6
4.3-5.9			0.998	0.032	33.8	16940	4468	4448	0.037	99.6
5.9-8			0.998	0.031	36.33	6759	1716	1710	0.035	99.7
8-12			0.999	0.024	42.55	2893	827	819	0.028	99
	12		0.999	0.022	46.69	1363	368	356	0.026	96.7

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5D4T

5d4t

Resolution: 2→42.798 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.62 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2275	3568	5 %
R_work	0.1982	67818	-
obs	0.1997	71386	99.67 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 106.6 Å² / B_iso mean: 33.9868 Å² / B_iso min: 14.27 Å²

Refinement step

Cycle: final / Resolution: 2→42.798 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8304	0	188	438	8930
B_iso mean	-	-	42.53	36.93	-
Num. residues	-	-	-	-	1028

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	8646
X-RAY DIFFRACTION	f_angle_d	0.797	11725
X-RAY DIFFRACTION	f_chiral_restr	0.032	1344
X-RAY DIFFRACTION	f_plane_restr	0.003	1464
X-RAY DIFFRACTION	f_dihedral_angle_d	12.507	3200

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4937	X-RAY DIFFRACTION	6.688	TORSIONAL
1	2	B	4937	X-RAY DIFFRACTION	6.688	TORSIONAL
1	3	C	4937	X-RAY DIFFRACTION	6.688	TORSIONAL
1	4	D	4937	X-RAY DIFFRACTION	6.688	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2-2.0274	0.3597	142	0.3248	2707	2849	99
2.0274-2.0564	0.3361	140	0.3031	2664	2804	99
2.0564-2.0871	0.2985	141	0.2833	2669	2810	99
2.0871-2.1197	0.27	143	0.2695	2724	2867	100
2.1197-2.1544	0.3065	142	0.2654	2692	2834	100
2.1544-2.1916	0.2796	142	0.2517	2690	2832	100
2.1916-2.2314	0.3135	141	0.2536	2696	2837	100
2.2314-2.2743	0.3071	145	0.2394	2745	2890	100
2.2743-2.3208	0.2576	139	0.2375	2645	2784	100
2.3208-2.3712	0.2618	142	0.2267	2692	2834	100
2.3712-2.4264	0.2702	144	0.2165	2737	2881	100
2.4264-2.487	0.2498	141	0.2127	2681	2822	100
2.487-2.5543	0.2516	143	0.2237	2716	2859	100
2.5543-2.6294	0.2756	144	0.2116	2744	2888	100
2.6294-2.7143	0.2464	142	0.2043	2689	2831	100
2.7143-2.8113	0.2133	142	0.2032	2696	2838	100
2.8113-2.9238	0.2439	143	0.2007	2718	2861	100
2.9238-3.0568	0.2483	143	0.2062	2729	2872	100
3.0568-3.218	0.2264	145	0.1997	2736	2881	100
3.218-3.4195	0.2291	141	0.1889	2683	2824	100
3.4195-3.6834	0.1961	144	0.1811	2749	2893	100
3.6834-4.0538	0.179	143	0.1632	2710	2853	100
4.0538-4.6398	0.181	145	0.1484	2760	2905	100
4.6398-5.8433	0.18	144	0.1656	2740	2884	99
5.8433-42.8076	0.1932	147	0.1729	2806	2953	99

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	3.5124	0.8942	-2.9419	1.7714	-2.4111	2.545	-0.1345	0.2662	-0.1649	-0.0033	0.0381	0.0339	0.0946	-1.0137	0.157	0.1786	-0.0267	-0.0359	0.175	-0.0364	0.2191	-7.3881	4.9368	19.0005
2	3.155	1.1312	-0.9673	4.5202	-0.6608	3.749	-0.02	-0.2037	0.0892	0.1452	-0.0954	0.6922	0.2037	-0.5589	0.1197	0.1814	0.0228	0.0261	0.3653	-0.0618	0.2955	-16.28	10.3131	37.6134
3	2.4377	-1.6338	-2.3308	5.4649	-0.3529	3.8952	-0.1105	-0.2837	0.1047	-0.0415	0.0428	0.4606	-0.2476	-0.4202	0.0019	0.2259	0.0352	-0.0281	0.358	-0.101	0.2889	-12.1518	19.5746	41.8228
4	2.8599	-0.6239	-1.0752	1.9866	0.5886	2.7266	-0.0603	-0.3956	-0.0629	0.3472	0.0184	0.0228	0.0595	0.0104	0.0437	0.2089	0.0219	-0.0033	0.2646	0.0199	0.1906	1.2146	6.0758	40.5539
5	4.5647	-2.7982	-6.2112	3.4345	5.5045	2.331	0.033	0.0749	-0.2398	-0.0601	-0.236	0.0608	-0.0946	-0.143	0.1742	0.2257	0.056	-0.0093	0.2709	0.0254	0.2088	4.0143	6.1142	16.9952
6	4.6262	-3.6052	-4.3445	5.7203	4.7104	6.9428	0.1465	-0.4071	0.4251	0.2554	0.3074	-0.3307	-0.3403	0.3472	-0.4489	0.2757	-0.0227	-0.0341	0.2768	-0.0032	0.2338	2.6422	14.1621	13.8835
7	5.2084	-1.0563	-2.7804	2.0531	6.598	2.1018	0.1873	0.1356	1.2229	-0.3329	-0.426	-0.262	-1.3199	0.1589	-0.2545	0.5693	-0.0587	-0.1203	0.3047	0.0063	0.4917	-6.4538	24.0462	20.4162
8	3.2613	-0.442	-3.6614	0.5902	-0.7714	2.0737	-0.0606	0.2584	0.0478	-0.1427	-0.0491	0.1762	-0.0585	-0.5468	-0.0276	0.1757	0.0141	-0.0464	0.2355	0.0095	0.2174	-0.5339	7.3605	4.3425
9	0.9641	0.2042	-1.6323	1.0884	-1.45	2.0845	-0.1598	-0.0466	-0.1862	-0.0706	0.038	0.0336	0.6295	-0.3044	0.1992	0.2168	0.0117	-0.0063	0.2175	0.0196	0.3036	-2.3606	-1.4934	22.7409
10	1.8055	0.1526	-1.4089	1.0191	-0.3374	5.4417	0.0766	-0.1851	0.0784	0.0197	0.0656	-0.2199	-0.1975	0.5583	-0.0375	0.1911	-0.0442	-0.0493	0.2431	0.0267	0.2664	32.7623	-3.8472	29.413
11	1.3921	0.3461	-1.185	1.8144	-1.2803	4.0214	0.0277	-0.3299	-0.1171	0.2535	-0.1954	-0.5012	-0.0478	0.5131	0.152	0.2399	0.0109	-0.052	0.3125	0.0574	0.2575	29.1005	-11.7939	50.9447
12	1.6392	-0.1543	0.7043	1.0283	-0.8158	3.6194	-0.0053	-0.2826	-0.0469	0.2589	0.0458	0.0747	-0.1339	-0.3433	-0.03	0.2318	0.0215	0.023	0.2119	0.005	0.1796	14.8384	-6.2892	45.7621
13	1.1952	-0.1045	-0.8785	0.75	0.0581	3.9369	-0.0461	-0.1085	-0.1297	0.0462	-0.0561	-0.1264	0.0656	0.1318	0.0681	0.1143	-0.0072	-0.0196	0.1621	-0.0052	0.1818	28.6688	-8.5755	23.9321
14	5.5878	-2.1035	-6.3427	2.447	3.0608	9.2876	0.3067	-0.5412	0.3371	0.08	0.1315	-0.2792	-0.5693	0.7907	-0.5336	0.2537	-0.0404	-0.0396	0.2037	-0.0075	0.2998	20.8414	20.2526	8.7549
15	4.6317	0.4967	-0.204	2.7503	0.3061	2.8801	-0.0193	0.0224	0.3987	-0.1999	0.0618	-0.0432	-0.3424	0.1671	-0.0358	0.3266	0.0041	0.0112	0.2045	0.0309	0.269	20.7526	24.9605	-11.2954
16	4.457	-0.8408	0.8078	1.7672	0.2085	4.0256	0.0106	0.6002	0.2977	-0.6822	0.0345	-0.0487	-0.1503	-0.0257	-0.0212	0.4434	-0.0094	0.0367	0.2636	0.0399	0.2705	16.6219	22.8295	-22.5456
17	1.569	0.9683	-1.1087	4.3197	-1.6575	3.6718	-0.1209	0.1356	-0.1946	-0.3621	0.0425	-0.2582	0.1496	0.1261	0.1014	0.195	0.0315	0.0061	0.1719	-0.0399	0.2418	19.5521	6.7346	-11.052
18	0.5629	-0.0961	-1.0907	0.048	0.3645	2.1122	0.0912	0.0459	-0.0651	0.0105	0.0013	0.0562	0.3099	0.2666	-0.0788	0.2327	0.0284	0.0126	0.1951	-0.0094	0.2508	14.3903	11.53	12.8122
19	3.5077	-0.7108	1.6038	3.6116	-4.0054	7.3436	0.0422	0.409	0.1428	-0.4818	0.2306	0.3295	0.3264	-0.6173	-0.0979	0.2603	-0.0202	0.0134	0.2508	-0.0441	0.3398	6.0983	20.5048	8.2053
20	2.9779	2.3063	-5.6224	6.1301	-5.4681	2.0587	0.1942	-0.2443	0.0969	0.5539	-0.0085	-0.0868	-1.0468	0.0657	-0.1112	0.3537	-0.0212	-0.0292	0.213	-0.0804	0.2863	12.5488	20.6656	22.9533
21	5.3444	-3.0716	-6.7817	4.7754	5.9752	2.4935	0.0591	-0.5077	0.0115	-0.0871	0.1998	-0.1788	-0.3995	1.0059	-0.2692	0.2615	-0.0013	-0.0262	0.3179	0.0386	0.3206	25.0381	12.3471	9.1124
22	0.6762	0.0952	-0.1603	1.4419	-0.6537	6.2541	0.0707	-0.0688	-0.1328	0.2038	0.0514	0.1329	0.6006	-0.4359	-0.1014	0.2655	-0.0356	0.0124	0.186	-0.0068	0.3164	16.7407	-22.2572	6.8823
23	5.2037	0.4424	2.1227	2.4933	1.1267	5.5251	0.0824	-0.1172	-0.4491	0.1745	-0.0445	0.109	0.6853	-0.0879	-0.0506	0.2436	0.0131	0.0261	0.1598	0.0048	0.2456	28.9292	-28.3842	-8.9124
24	2.1876	-1.5398	-0.8849	1.6652	0.2475	2.3801	0.0143	0.0724	-0.0475	-0.1264	-0.0532	-0.2572	0.0757	0.2184	0.064	0.1937	0.0202	-0.0089	0.2109	0.0019	0.249	38.1109	-22.3041	-14.7462
25	1.4178	-1.0686	-0.7129	2.0629	2.0921	4.8925	0.0471	0.0472	0.1136	-0.1681	0.0164	-0.1202	-0.2578	0.1728	-0.075	0.1703	-0.0067	-0.0024	0.1571	0.0052	0.2269	28.1411	-9.2984	-11.5059
26	3.45	0.6233	-2.8806	1.0788	-1.4889	2.5719	0.0866	-0.2237	-0.0305	0.1529	-0.0976	0.1336	-0.1299	0.1831	0.0499	0.1847	-0.0236	-0.0096	0.1787	-0.0198	0.1584	19.8961	-10.9925	9.6525
27	5.3161	-3.5279	-3.3611	4.8951	3.4438	5.3387	-0.0061	-0.0728	0.1518	0.0333	0.15	-0.4812	0.2179	0.7768	-0.142	0.3022	-0.0306	-0.0521	0.3175	0.0659	0.2945	28.2554	-21.5477	14.9567
28	0.8573	0.3619	-0.4074	1.4704	-1.7507	2.5038	-0.0416	-0.0251	-0.1029	-0.0243	0.0242	0.1977	0.5874	-0.5292	-0.1139	0.1935	-0.0314	-0.012	0.1951	-0.0169	0.2597	13.2763	-16.4914	10.0691

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 42 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 77 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 78 through 130 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 131 through 184 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 185 through 202 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 203 through 221 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 222 through 233 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 234 through 246 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 247 through 268 )	A
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 12 through 42 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 43 through 105 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 106 through 184 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 185 through 268 )	B
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 12 through 42 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 43 through 92 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 93 through 116 )	C
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 117 through 184 )	C
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 185 through 202 )	C
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 203 through 233 )	C
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 234 through 246 )	C
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 247 through 268 )	C
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 12 through 42 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 43 through 92 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 93 through 130 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 131 through 175 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 176 through 201 )	D
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 202 through 234 )	D
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 235 through 268 )	D

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