PDB-5d5t: SeMet-labelled HcgC from Methanocaldococcus jannaschii in P1 spac...

ID or keywords:

Entry

Database: PDB / ID: 5d5t

Title

SeMet-labelled HcgC from Methanocaldococcus jannaschii in P1 space group

Components

Uncharacterized protein MJ0489

Keywords

UNKNOWN FUNCTION / Rossmann-like fold

Function / homology

FeGP cofactor biosynthesis protein, methyltransferase HcgC / FeGP cofactor biosynthesis protein, methyltransferase HcgC / Uncharacterized protein MJ0489

Function and homology information

Biological species

Methanocaldococcus jannaschii (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 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 11, 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
Revision 1.3	Oct 9, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5d5t.cif.gz	409.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5d5t.ent.gz	339.1 KB	Display	PDB format
PDBx/mmJSON format	5d5t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5d5t_validation.pdf.gz	448.7 KB	Display	wwPDB validaton report
Full document	5d5t_full_validation.pdf.gz	454.6 KB	Display
Data in XML	5d5t_validation.xml.gz	37.7 KB	Display
Data in CIF	5d5t_validation.cif.gz	52.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5t ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5t	HTTPS FTP

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Related structure data

Related structure data	5d4tSC 5d4uC 5d4vC 5d5oC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5d4t-1 5d4t-2 5d5o-1 5d4t-4 2d5c-d 2cy0-d 5d4t-3 2ev9-d 3sef-2 5fwn-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

Deposited unit

A: Uncharacterized protein MJ0489

B: Uncharacterized protein MJ0489

C: Uncharacterized protein MJ0489

D: Uncharacterized protein MJ0489

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

1

A: Uncharacterized protein MJ0489

B: Uncharacterized protein MJ0489

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

2

C: Uncharacterized protein MJ0489

D: Uncharacterized protein MJ0489

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

Unit cell

Length a, b, c (Å)	45.480, 76.990, 84.990
Angle α, β, γ (deg.)	108.090, 89.980, 105.380
Int Tables number	1
Space group name H-M	P1

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: 30847.480 Da / Num. of mol.: 4 / Fragment: Rossmann-like domain, residues 2-268 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 373 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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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: 44.13 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 22.5 % (w/v) PEP426, 90 mM HEPES-NaOH (pH 7.5), 45 mM magnesium chloride and 0.2 M 2,2,2-trifluoroethanol

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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: Aug 29, 2013

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: 2.4→50 Å / Num. obs: 78917 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / B_iso Wilson estimate: 27.16 Å² / R_merge F obs: 0.994 / R_merge(I) obs: 0.094 / R_rim(I) all: 0.111 / Χ²: 1.027 / Net I/σ(I): 9.52 / Num. measured all: 272312

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	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
2.4-2.5		0.864	0.415	2.74	28936	9450	8910	0.501	94.3
2.5-2.6		0.916	0.368	3.32	28034	8146	7880	0.434	96.7
2.6-2.7		0.937	0.29	4.04	23198	6934	6682	0.345	96.4
2.7-3		0.969	0.198	5.56	51569	15654	15094	0.235	96.4
3-3.5		0.989	0.11	9.35	51575	15618	14937	0.131	95.6
3.5-4.5		0.994	0.062	15.6	46893	14084	13472	0.074	95.7
4.5-5		0.996	0.05	19.35	11269	3388	3237	0.059	95.5
5-5.5		0.996	0.052	19.46	7970	2274	2190	0.061	96.3
5.5-6		0.995	0.056	17.91	5427	1578	1505	0.066	95.4
6-6.5		0.995	0.056	18.11	3570	1136	1087	0.067	95.7
6.5-7		0.994	0.055	19.58	2628	796	761	0.065	95.6
7-7.5		0.993	0.051	19.56	1978	616	591	0.061	95.9
7.5-8		0.996	0.05	21.8	1692	480	452	0.058	94.2
8-12		0.994	0.046	24.48	5274	1572	1481	0.054	94.2
	12	0.994	0.047	25.17	2299	662	638	0.055	96.4

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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: 5D4T

5d4t

Resolution: 2.4→42.837 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 27.09 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2511	2020	5 %
R_work	0.205	38410	-
obs	0.2074	40430	98.27 %

Solvent computation

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

Displacement parameters

B_iso max: 103.3 Å² / B_iso mean: 36.6985 Å² / B_iso min: 6.27 Å²

Refinement step

Cycle: final / Resolution: 2.4→42.837 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7884	0	0	373	8257
B_iso mean	-	-	-	32.39	-
Num. residues	-	-	-	-	976

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	8038
X-RAY DIFFRACTION	f_angle_d	0.84	10879
X-RAY DIFFRACTION	f_chiral_restr	0.034	1273
X-RAY DIFFRACTION	f_plane_restr	0.004	1370
X-RAY DIFFRACTION	f_dihedral_angle_d	12.609	2981

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	4558	X-RAY DIFFRACTION	9.236	TORSIONAL
1	2	B	4558	X-RAY DIFFRACTION	9.236	TORSIONAL
1	3	C	4558	X-RAY DIFFRACTION	9.236	TORSIONAL
1	4	D	4558	X-RAY DIFFRACTION	9.236	TORSIONAL

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4-2.46	0.3416	139	0.2834	2649	2788	96
2.46-2.5265	0.331	146	0.2686	2781	2927	98
2.5265-2.6009	0.352	144	0.2574	2737	2881	98
2.6009-2.6848	0.2617	145	0.2454	2756	2901	98
2.6848-2.7807	0.2819	142	0.2341	2684	2826	98
2.7807-2.892	0.2797	146	0.2281	2775	2921	98
2.892-3.0236	0.3207	146	0.2246	2781	2927	98
3.0236-3.183	0.2702	142	0.2204	2698	2840	99
3.183-3.3823	0.2665	146	0.2085	2767	2913	98
3.3823-3.6434	0.2475	145	0.1891	2760	2905	99
3.6434-4.0098	0.2323	145	0.1834	2760	2905	99
4.0098-4.5894	0.213	145	0.1584	2753	2898	98
4.5894-5.7799	0.1849	144	0.1696	2735	2879	99
5.7799-42.8436	0.2031	145	0.1989	2774	2919	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	2.4577	-0.8537	5.1227	0.7613	-2.8319	2.1078	-0.0345	-0.2881	0.167	0.0901	-0.0313	0.1261	-0.0258	-1.5257	0.2713	0.3532	0.0995	0.0026	0.3653	-0.0828	0.3116	-2.4988	59.3366	150.8996
2	4.0771	-1.2432	1.515	5.0466	1.187	3.0125	-0.1879	0.0305	0.6295	-0.1009	-0.1998	0.273	-0.6016	-0.1837	0.4246	0.5156	-0.0054	-0.0919	0.1996	0.011	0.2994	8.6898	69.5569	170.053
3	1.2234	0.6416	-0.6992	2.6869	1.6437	4.393	-0.2744	-0.13	-0.1368	0.1082	-0.0224	-0.164	0.3661	0.2876	0.2263	0.2267	0.0213	0.0229	0.1391	0.0367	0.2306	17.0149	55.0944	161.5303
4	0.843	-0.5316	1.1634	0.6312	-0.4809	5.2736	-0.244	-0.0782	0.2634	0.1533	-0.119	0.001	-0.647	-0.5819	0.343	0.247	0.0525	-0.016	0.2005	-0.037	0.3344	2.3207	60.4669	144.0181
5	0.7731	0.6778	2.6273	1.1246	2.4691	6.4298	-0.182	0.1847	0.1674	-0.0266	-0.1283	-0.2613	-1.0036	1.2013	0.1589	0.4004	-0.154	-0.0114	0.3877	0.1013	0.3109	17.1336	65.3431	124.6441
6	6.9139	-0.6326	3.6068	5.9173	-0.3086	5.0542	-0.2174	-0.2008	0.6942	0.4704	-0.0885	-0.1752	-0.7561	0.0065	0.3278	0.5211	0.0126	-0.0121	0.2528	0.0491	0.3028	4.4058	70.8346	106.5132
7	1.5501	-0.9835	0.9534	3.3619	-1.9313	5.7658	-0.0153	0.2545	-0.0577	-0.1349	-0.0838	0.3314	0.0123	-0.1731	0.0581	0.1787	0.0103	0.0198	0.2139	-0.0152	0.2157	1.504	56.1324	109.2992
8	0.7316	0.2361	0.282	1.674	1.0675	4.9585	0.0186	0.0266	0.2316	-0.1759	-0.1607	0.1231	-0.6567	0.1859	0.1193	0.3423	-0.0657	0.0041	0.1763	0.0499	0.3063	12.4361	63.7455	131.6947
9	1.3586	0.2819	2.6177	1.2438	1.0989	7.2325	-0.0469	-0.1776	0.0103	-0.1057	-0.1477	0.2702	0.4072	-0.6603	0.1916	0.232	-0.0569	0.0121	0.1976	-0.0036	0.3196	0.4972	24.8053	124.5738
10	6.9131	2.3997	7.3881	9.6828	1.6225	7.9778	0.2359	-0.3599	-0.3552	1.2687	0.1334	-0.5539	0.8507	-0.2925	-0.3044	0.6539	0.0202	0.0281	0.3224	0.0243	0.2765	0.5782	19.1138	117.9271
11	4.2814	0.9221	-0.411	4.4169	2.0629	5.9625	-0.3718	0.3045	-1.0641	-0.5406	0.4933	-1.127	0.4044	0.6474	-0.1519	0.476	0.0145	0.1325	0.3378	-0.1195	0.5	8.909	14.7927	106.9162
12	2.9165	1.8468	1.7187	3.9203	2.2468	2.5824	-0.4891	0.5098	0.021	-0.8065	0.3403	-0.0117	-0.3512	0.291	0.1458	0.3844	-0.0603	-0.0234	0.193	0.0225	0.2234	7.3085	32.3362	109.1548
13	1.5377	0.895	2.159	1.5037	0.4513	5.0353	0.0018	0.0633	-0.2445	-0.1229	-0.0544	-0.0805	0.2293	-0.0766	0.0646	0.1849	-0.0144	0.0295	0.1357	0.0052	0.2534	9.0902	28.5382	134.9354
14	1.145	0.4038	2.262	1.717	2.261	7.7305	-0.0379	0.4359	-0.0262	-0.2056	0.1196	-0.2465	0.0853	1.2395	-0.0997	0.1938	0.015	0.0155	0.3394	-0.0212	0.3155	31.5936	34.6072	143.3629
15	5.2748	-0.5776	2.6184	4.2421	0.0466	4.7793	0.3331	0.576	-0.3203	-0.2533	0.1036	-0.1439	0.2837	0.7071	-0.2696	0.364	0.1454	-0.0225	0.327	-0.0407	0.3201	36.5158	30.4656	161.487
16	4.0099	4.7086	-3.7209	7.2891	-1.9995	6.6357	-0.3565	-0.365	-0.6837	0.361	0.3316	-0.0334	0.4552	-0.153	-0.1346	0.4656	0.1429	-0.0471	0.3612	0.0999	0.4437	30.8707	21.1867	167.6246
17	4.1051	-1.1307	2.1221	2.5923	-0.467	3.0391	-0.2582	-0.6923	-0.0639	0.4902	0.3518	-0.0236	0.1909	-0.1869	-0.0444	0.2592	0.088	-0.0338	0.2443	-0.0352	0.2531	23.2099	36.7779	165.4698
18	1.5955	-0.7683	1.6243	1.2474	0.2913	4.4872	-0.052	0.0297	-0.1853	0.0154	0.0709	-0.1323	0.2637	0.4552	-0.0218	0.1297	0.0458	0.0344	0.2301	-0.0236	0.2887	23.9562	32.7016	139.704

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 13 through 42 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 43 through 139 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 140 through 184 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 185 through 268 )	A
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 13 through 42 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 43 through 105 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 106 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 13 through 55 )	C
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 56 through 69 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 70 through 105 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 106 through 184 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 185 through 268 )	C
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 13 through 42 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 43 through 69 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 70 through 105 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 106 through 184 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 185 through 268 )	D

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