PDB-5d4v: HcgC with SAH and a guanylylpyridinol (GP) derivative

ID or keywords:

Entry

Database: PDB / ID: 5d4v

Title

HcgC with SAH and a guanylylpyridinol (GP) derivative

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-ADENOSYL-L-HOMOCYSTEINE / Chem-YGP / Uncharacterized protein MJ0489

Function and homology information

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 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	5d4v.cif.gz	453 KB	Display	PDBx/mmCIF format
PDB format	pdb5d4v.ent.gz	371.1 KB	Display	PDB format
PDBx/mmJSON format	5d4v.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/d4/5d4v ftp://data.pdbj.org/pub/pdb/validation_reports/d4/5d4v	HTTPS FTP

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Related structure data

Related structure data	5d4tC 5d4uSC 5d5oC 5d5tC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5d4u-1 5d5o-3 5d4u-2 4j30-1 3th1-2 1zyc-1 1zxe-1 4j32-1 5d5o-2 5d5o-4 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

Deposited unit

A: Uncharacterized protein MJ0489

B: Uncharacterized protein MJ0489

C: Uncharacterized protein MJ0489

D: Uncharacterized protein MJ0489

hetero molecules

126 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
63.2 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
63.2 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.110, 70.480, 91.770
Angle α, β, γ (deg.)	90.000, 105.190, 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-SAH / S-ADENOSYL-L-HOMOCYSTEINE / 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 / Sulfate Mass: 96.063 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-YGP / 5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine Mass: 484.357 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₆O₉P
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.2 Å³/Da / Density % sol: 44.04 %
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: 1.6→50 Å / Num. obs: 139537 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / B_iso Wilson estimate: 22.9 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.048 / R_rim(I) all: 0.055 / Χ²: 0.996 / Net I/σ(I): 15.99 / Num. measured all: 622756

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
1.6-1.7		4.4	0.704	0.802	2.26	101483	23152	23076	0.911	99.7
1.7-1.9			0.915	0.37	4.7	146402	32936	32891	0.421	99.9
1.9-2.2			0.987	0.123	11.86	133869	29625	29584	0.14	99.9
2.2-2.5			0.996	0.063	20.25	78452	17119	17100	0.071	99.9
2.5-2.7			0.997	0.046	25.62	34305	7587	7571	0.052	99.8
2.7-3			0.998	0.037	29.98	33761	7890	7867	0.042	99.7
3-3.3			0.998	0.032	36.43	24325	5314	5302	0.036	99.8
3.3-3.5			0.998	0.029	41.54	11618	2593	2585	0.033	99.7
3.5-3.8			0.998	0.028	42.55	12859	2929	2921	0.032	99.7
3.8-4			0.999	0.027	40.89	6141	1519	1509	0.031	99.3
4-4.3			0.998	0.027	42.73	7070	1780	1772	0.031	99.6
4.3-5.9			0.998	0.028	46.78	20242	4481	4463	0.032	99.6
5.9-8			0.998	0.029	42.52	7013	1720	1711	0.033	99.5
8-12			0.999	0.028	45.91	3647	828	827	0.032	99.9
	12		0.998	0.031	46.55	1569	371	358	0.034	96.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5D4U

5d4u

Resolution: 1.6→44.283 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2079	6977	5 %
R_work	0.1706	132554	-
obs	0.1724	139531	99.83 %

Solvent computation

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

Displacement parameters

B_iso max: 119.41 Å² / B_iso mean: 31.7103 Å² / B_iso min: 11.98 Å²

Refinement step

Cycle: final / Resolution: 1.6→44.283 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8342	0	260	937	9539
B_iso mean	-	-	52.47	40.76	-
Num. residues	-	-	-	-	1034

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	8779
X-RAY DIFFRACTION	f_angle_d	1.446	11927
X-RAY DIFFRACTION	f_chiral_restr	0.074	1368
X-RAY DIFFRACTION	f_plane_restr	0.007	1478
X-RAY DIFFRACTION	f_dihedral_angle_d	13.447	3229

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4974	X-RAY DIFFRACTION	7.474	TORSIONAL
1	2	B	4974	X-RAY DIFFRACTION	7.474	TORSIONAL
1	3	C	4974	X-RAY DIFFRACTION	7.474	TORSIONAL
1	4	D	4974	X-RAY DIFFRACTION	7.474	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6-1.6182	0.3269	230	0.2977	4372	4602	99
1.6182-1.6372	0.3196	233	0.2774	4422	4655	100
1.6372-1.6572	0.3516	228	0.2837	4347	4575	100
1.6572-1.6782	0.2809	235	0.2651	4456	4691	100
1.6782-1.7002	0.3037	229	0.2578	4360	4589	100
1.7002-1.7235	0.2801	233	0.2458	4430	4663	100
1.7235-1.7482	0.2696	229	0.2411	4333	4562	100
1.7482-1.7743	0.2676	233	0.2217	4443	4676	100
1.7743-1.802	0.2357	231	0.2195	4391	4622	100
1.802-1.8315	0.2747	234	0.2243	4431	4665	100
1.8315-1.8631	0.275	230	0.2181	4383	4613	100
1.8631-1.897	0.2484	233	0.2077	4421	4654	100
1.897-1.9335	0.247	231	0.1937	4391	4622	100
1.9335-1.9729	0.2273	231	0.189	4394	4625	100
1.9729-2.0158	0.2219	234	0.1751	4444	4678	100
2.0158-2.0627	0.2165	233	0.1841	4412	4645	100
2.0627-2.1143	0.2196	232	0.1734	4407	4639	100
2.1143-2.1715	0.2054	230	0.1679	4372	4602	100
2.1715-2.2354	0.2126	233	0.1691	4440	4673	100
2.2354-2.3075	0.2224	233	0.1654	4421	4654	100
2.3075-2.39	0.2102	233	0.1709	4434	4667	100
2.39-2.4857	0.2242	232	0.1643	4394	4626	100
2.4857-2.5988	0.2113	233	0.1688	4441	4674	100
2.5988-2.7358	0.2208	233	0.1718	4421	4654	100
2.7358-2.9072	0.1983	233	0.1693	4419	4652	100
2.9072-3.1316	0.2086	233	0.1689	4435	4668	100
3.1316-3.4466	0.187	234	0.1612	4454	4688	100
3.4466-3.9451	0.1801	235	0.1422	4458	4693	100
3.9451-4.9693	0.1604	235	0.1298	4472	4707	100
4.9693-44.2995	0.1836	241	0.1591	4556	4797	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	0.6788	-0.33	-0.5029	0.9829	1.0564	3.5499	-0.0524	-0.0584	-0.0689	0.0312	-0.1326	0.2717	-0.0745	-0.4529	0.1944	0.1778	0.0275	-0.0204	0.2754	-0.0269	0.296	-13.0961	12.5038	33.5857
2	5.9718	-1.0588	-2.9281	1.2762	0.5847	3.3307	-0.166	-0.7409	-0.0934	0.3297	0.1307	-0.0009	0.0597	0.247	0.0236	0.2567	0.0675	-0.0095	0.2965	0.0164	0.1749	-0.057	9.868	44.9904
3	1.2871	-0.2879	-0.7278	0.5679	0.2299	2.5931	-0.0671	-0.0164	-0.0623	0.0121	-0.0305	0.1165	-0.0159	-0.0202	0.098	0.1371	0.0096	-0.0264	0.1557	-0.019	0.212	0.059	7.798	19.409
4	4.276	-0.9817	-3.7458	4.2688	2.7342	2.0309	0.1687	0.3243	0.0311	-0.6911	0.2736	-0.4834	-0.1715	0.7487	-0.3633	0.2579	-0.0029	0.0388	0.4051	-0.0076	0.2877	39.6502	-10.0677	11.6058
5	0.7579	-0.2363	-0.6495	1.8849	0.1564	3.0896	0.0972	-0.311	0.0534	0.2849	-0.0873	-0.2817	-0.22	0.4548	-0.0129	0.2263	-0.044	-0.0224	0.3703	0.0229	0.228	29.1671	-4.4566	45.9567
6	1.2267	-1.2825	0.211	5.2095	0.5882	5.7212	0.0749	-0.4314	-0.1149	0.1735	-0.0572	-0.6472	0.1205	0.7947	-0.0299	0.205	-0.0022	-0.0085	0.4627	0.1115	0.2882	27.3132	-16.4786	53.5368
7	1.8371	0.0729	1.0655	2.0165	-0.2247	3.3957	0.011	-0.4121	-0.0551	0.3543	0.0027	0.167	-0.0739	-0.2522	-0.0036	0.1787	0.0395	0.0508	0.243	0.0236	0.1572	13.2918	-5.7212	43.6509
8	1.11	-0.079	-1.0871	0.6766	0.5269	3.7683	-0.0601	-0.1299	-0.0984	0.0689	0.0387	-0.041	0.1392	0.099	0.0058	0.1031	0.001	-0.0086	0.1807	0.0063	0.1543	28.6342	-8.6414	23.9371
9	6.5712	-0.8023	-7.0171	3.054	1.0586	2.0911	0.09	-0.7264	0.2833	0.516	0.0518	-0.0106	-0.4114	0.6255	-0.3185	0.3475	-0.0493	-0.0516	0.3535	-0.0796	0.3045	10.555	23.2751	26.1914
10	6.2676	-2.5914	-7.683	1.3547	3.0563	2.367	0.3633	-0.3515	0.7013	-0.1676	0.1924	-0.3882	-0.5413	0.651	-0.4359	0.2474	-0.0254	-0.0095	0.3481	-0.0183	0.3014	25.3899	18.5745	-0.0059
11	4.1753	-0.4851	-1.0546	3.2224	-0.657	4.098	0.0385	0.0136	0.4098	-0.101	0.1719	-0.1703	-0.2523	0.2658	-0.1645	0.2425	-0.0461	0.0134	0.1945	0.0071	0.2365	24.2353	23.3768	-12.1381
12	3.5894	-0.5647	-0.4658	3.068	-0.7024	3.6282	0.0463	0.2829	0.3874	-0.3057	0.2055	0.3257	-0.3722	-0.3391	-0.2598	0.2568	-0.0226	-0.0111	0.2081	0.1042	0.2908	15.4415	24.9689	-17.9333
13	2.2565	1.3705	-1.7091	3.8152	-1.8995	3.2427	-0.1801	0.1562	-0.1479	-0.3368	0.1348	-0.0852	0.184	0.0172	0.0531	0.1968	0.0098	-0.0224	0.145	-0.019	0.2013	19.8699	6.7364	-11.1167
14	0.6248	0.2294	-1.0576	0.2813	0.2747	8.8959	0.0089	-0.0431	-0.0481	-0.0439	0.0071	-0.0229	0.3178	0.1502	-0.0118	0.1962	0.0103	-0.0161	0.1615	-0.0034	0.2466	14.3544	11.3609	12.7668
15	0.7195	0.137	-0.3454	1.0294	-0.8755	4.8364	0.047	0.0488	0.1735	-0.0396	0.0614	0.0684	-0.3604	-0.1859	-0.0967	0.2049	0.0215	-0.0104	0.1537	-0.015	0.2414	7.8877	20.4896	11.8458
16	2.0224	-0.5532	-2.8253	1.6296	1.8952	8.5756	-0.0338	-0.3953	0.0724	0.0508	0.2599	-0.2083	0.1507	1.0856	-0.0576	0.1464	-0.0079	-0.0311	0.2635	-0.0332	0.2208	25.0966	12.6366	9.0605
17	0.7524	-0.236	-0.6824	0.952	-1.1088	9.9363	0.0168	-0.1059	-0.1516	0.1417	0.1307	0.1626	0.5881	-0.6955	-0.1252	0.1892	-0.0532	0.0237	0.1535	0.0279	0.2184	16.7852	-22.0834	6.7674
18	5.0206	0.8025	2.3852	2.207	1.0441	5.2664	0.0596	-0.1746	-0.444	0.1474	0.0437	0.0386	0.4845	-0.0166	-0.1017	0.1862	0.0226	0.0298	0.1305	0.0069	0.2099	28.9061	-28.1523	-9.1553
19	2.3641	-1.6089	-1.1425	2.1959	0.1689	2.3782	0.0373	0.0203	-0.0383	-0.1226	-0.0561	-0.2988	0.049	0.2993	0.0317	0.1439	0.0067	0.0014	0.1778	0.0029	0.1917	38.136	-22.2641	-15.006
20	1.3093	-0.7927	-1.1052	3.4316	3.416	6.0243	0.0084	-0.0404	0.0872	-0.2557	-0.0059	-0.0707	-0.5052	0.2507	-0.0472	0.1415	-0.0113	-0.0015	0.1276	0.0249	0.1384	29.7641	-8.6381	-9.1197
21	3.51	0.4215	-0.0114	5.4195	4.4284	2.0496	-0.0425	0.3606	0.1743	-0.5828	-0.0098	-0.0531	-0.6501	0.2436	-0.0567	0.2333	-0.0261	0.0288	0.2217	0.0272	0.1822	30.8938	-8.8753	-17.6129
22	1.3522	-0.3119	-0.8444	2.4304	2.1328	4.9312	-0.0173	-0.0101	-0.0377	0.1183	-0.1486	0.2542	-0.172	-0.3393	0.2487	0.1193	0.0052	0.0156	0.1174	0.0028	0.1619	21.0962	-9.0497	-2.5423
23	2.2238	-1.6604	-3.2039	0.8827	1.4644	7.0285	0.0648	-0.129	0.137	0.0707	0.0072	0.0682	-0.1745	0.0415	-0.1139	0.174	-0.0244	0.0078	0.1561	0.0063	0.1574	19.657	-12.7951	12.435
24	8.6041	-2.4659	-4.581	2.3894	1.6347	3.9289	0.1421	0.02	-0.0112	-0.0891	-0.0603	-0.1893	0.0682	0.1498	-0.0721	0.2313	-0.018	0.0038	0.1979	0.0318	0.2178	24.331	-17.2281	17.4804
25	8.2311	-2.8329	-6.0384	2.2763	2.8657	6.8606	-0.276	-0.3105	-0.4852	0.2917	0.134	-0.0329	0.5948	0.4641	0.1441	0.3212	0.0328	-0.0207	0.2085	0.0612	0.254	25.1226	-24.1606	16.3602
26	3.4495	2.5357	-4.0395	4.3817	-4.8943	2.556	0.019	0.1686	0.1214	-0.0514	0.2547	0.3564	0.3571	-0.8076	-0.2656	0.1888	-0.0348	-0.0209	0.2065	-0.0079	0.2359	13.0341	-14.5932	3.4305

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 116 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 117 through 166 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 167 through 268 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 9 through 22 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 23 through 77 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 78 through 116 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 117 through 184 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 185 through 268 )	B
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 9 through 22 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 23 through 42 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 43 through 77 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 78 through 116 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 117 through 184 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 185 through 202 )	C
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 203 through 246 )	C
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 247 through 268 )	C
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 12 through 42 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 43 through 92 )	D
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 93 through 130 )	D
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 131 through 152 )	D
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 153 through 166 )	D
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 167 through 184 )	D
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 185 through 201 )	D
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 202 through 221 )	D
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 222 through 246 )	D
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 247 through 268 )	D

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