PDB-5d5p: HcgB from Methanococcus maripaludis

ID or keywords:

Entry

Database: PDB / ID: 5d5p

Title

HcgB from Methanococcus maripaludis

Components

HcgB

Keywords

TRANSFERASE / Guanylyltransferase

Function / homology

Function and homology information

FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / Helix hairpin bin / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology

Biological species

Methanococcus maripaludis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

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

Funding support

Japan,

Germany, 2items

Citation

Journal: Faraday Discuss. / Year: 2017
Title: Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase.
Authors: Bai, L. / Fujishiro, T. / Huang, G. / Koch, J. / Takabayashi, A. / Yokono, M. / Tanaka, A. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.

History

Deposition	Aug 11, 2015	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Oct 26, 2016	Provider: repository / Type: Initial release
Revision 1.1	Mar 29, 2017	Group: Database references
Revision 1.2	Jun 14, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	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	5d5p.cif.gz	253.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5d5p.ent.gz	206.7 KB	Display	PDB format
PDBx/mmJSON format	5d5p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5d5p_validation.pdf.gz	437.2 KB	Display	wwPDB validaton report
Full document	5d5p_full_validation.pdf.gz	441.3 KB	Display
Data in XML	5d5p_validation.xml.gz	26.5 KB	Display
Data in CIF	5d5p_validation.cif.gz	38.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d5/5d5p ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d5p	HTTPS FTP

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Related structure data

Related structure data	5d5qC 3wb1S 3brc 3wb0 3wb2 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4mpq-d 5kz6-2 4bzf-1 5sux-d 1naq-2 2xul-1 4gvg-1 5d5q-1 3n13-d 4od5-4 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: HcgB

B: HcgB

C: HcgB

D: HcgB

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

1

A: HcgB

C: HcgB

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

2

B: HcgB

D: HcgB

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

Unit cell

Length a, b, c (Å)	64.120, 72.540, 70.980
Angle α, β, γ (deg.)	90.000, 99.090, 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 AA
2	1	chain B and segid BA
3	1	chain C and segid CA
4	1	chain D and segid DA

NCS domain segments:

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

#1: Protein	HcgB Mass: 18282.047 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanococcus maripaludis (strain S2 / LL) (archaea) Gene: MMP1497 / Plasmid: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6LX55
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 359 / 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: 44.82 %
Crystal grow	Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 0.1 M CAPS (pH 10.5), 0.2 M NaCl, 20 % (w/v) PEG8000

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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 23, 2014

Radiation

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

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 70410 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / B_iso Wilson estimate: 25.49 Å² / R_merge F obs: 0.999 / R_merge(I) obs: 0.045 / R_rim(I) all: 0.052 / Χ²: 1.048 / Net I/σ(I): 18.08 / Num. measured all: 272465

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
1.7-1.8		0.729	0.73	2.55	43002	11053	11005	0.848	99.6
1.8-2		0.937	0.322	5.65	62699	16072	16036	0.374	99.8
2-2.3		0.985	0.123	12.63	57204	14839	14807	0.143	99.8
2.3-2.8		0.996	0.056	22.78	49974	12721	12691	0.065	99.8
2.8-3.3		0.998	0.032	33.73	23608	6174	6139	0.037	99.4
3.3-4.3		0.999	0.024	42.54	19258	5346	5286	0.028	98.9
4.3-5.9		0.999	0.02	53.78	10492	2732	2718	0.024	99.5
5.9-8		0.999	0.02	54.16	3569	1039	1021	0.024	98.3
8-12		0.999	0.016	63.76	1879	496	494	0.019	99.6
	12	0.999	0.018	62.1	780	222	213	0.021	95.9

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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: 3WB1

3wb1

Resolution: 1.7→43.675 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.92 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.215	3520	5 %
R_work	0.1849	66882	-
obs	0.1864	70402	99.62 %

Solvent computation

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

Displacement parameters

B_iso max: 98.73 Å² / B_iso mean: 34.1479 Å² / B_iso min: 14.68 Å²

Refinement step

Cycle: final / Resolution: 1.7→43.675 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4729	0	0	359	5088
B_iso mean	-	-	-	39.17	-
Num. residues	-	-	-	-	627

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	4783
X-RAY DIFFRACTION	f_angle_d	1.351	6465
X-RAY DIFFRACTION	f_chiral_restr	0.064	825
X-RAY DIFFRACTION	f_plane_restr	0.008	816
X-RAY DIFFRACTION	f_dihedral_angle_d	11.772	1849

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Rms	Type
1	1	A	2916	X-RAY DIFFRACTION	4.651	TORSIONAL
1	2	B	2916	X-RAY DIFFRACTION	4.651	TORSIONAL
1	3	C	2916	X-RAY DIFFRACTION	4.651	TORSIONAL
1	4	D	2916	X-RAY DIFFRACTION	4.651	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 (%)
1.7-1.7233	0.3079	140	0.3015	2656	2796	100
1.7233-1.7479	0.3283	139	0.277	2646	2785	99
1.7479-1.774	0.272	141	0.2699	2680	2821	99
1.774-1.8017	0.3702	138	0.2719	2614	2752	100
1.8017-1.8313	0.3142	142	0.2657	2700	2842	100
1.8313-1.8628	0.2811	140	0.2428	2665	2805	100
1.8628-1.8967	0.2644	140	0.2329	2663	2803	100
1.8967-1.9332	0.2608	140	0.2159	2656	2796	100
1.9332-1.9727	0.265	141	0.2139	2682	2823	100
1.9727-2.0155	0.2482	141	0.2128	2678	2819	100
2.0155-2.0624	0.2069	140	0.2016	2665	2805	100
2.0624-2.114	0.2234	141	0.1992	2673	2814	100
2.114-2.1712	0.2129	140	0.1928	2660	2800	100
2.1712-2.2351	0.2431	143	0.1855	2709	2852	100
2.2351-2.3072	0.1973	140	0.1895	2664	2804	100
2.3072-2.3896	0.27	140	0.1906	2670	2810	100
2.3896-2.4853	0.2036	141	0.1872	2678	2819	100
2.4853-2.5984	0.2208	142	0.1845	2684	2826	100
2.5984-2.7354	0.2573	141	0.1896	2689	2830	100
2.7354-2.9067	0.1976	141	0.1912	2680	2821	99
2.9067-3.1311	0.2328	140	0.1913	2664	2804	100
3.1311-3.4461	0.2335	142	0.1896	2698	2840	100
3.4461-3.9445	0.1716	141	0.1651	2674	2815	99
3.9445-4.9685	0.1669	142	0.1371	2687	2829	99
4.9685-43.689	0.1772	144	0.164	2747	2891	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	2.0677	-2.3437	-1.9381	9.7206	-0.2021	4.4756	0.005	-1.1339	-0.9434	0.7956	-0.424	0.6506	0.3641	0.1535	0.3376	0.4498	0.0282	0.1249	0.5759	0.078	0.552	20.8033	-14.19	36.5571
2	3.0675	-0.1055	-0.4083	4.0887	-2.2818	6.1994	0.0047	-0.2532	0.3578	0.4043	0.2109	0.4193	-0.7525	-0.4305	-0.2358	0.2229	0.0485	0.047	0.2217	-0.0422	0.2804	11.8355	6.2415	23.9587
3	2.0464	0.0221	-0.2067	2.1004	0.7617	3.0725	0.0512	0.0734	0.2521	-0.094	-0.0319	0.2122	-0.1701	-0.2872	-0.0207	0.1385	0.0459	0.0066	0.1517	0.0334	0.1796	15.1553	-1.3822	15.3276
4	6.8348	0.9393	-2.2962	2.041	1.0464	2.0057	-0.3302	-0.5157	-1.2111	0.2659	0.1301	0.5885	1.1473	-0.0257	0.1809	0.4943	0.096	0.0968	0.2551	0.07	0.4851	34.5376	-29.3486	20.3511
5	8.2077	0.1698	-3.9586	5.871	-3.4619	2.0088	-0.2719	-1.0378	-0.4186	0.6718	0.0129	-0.3501	0.7797	0.9032	0.2738	0.3719	0.0889	-0.0321	0.2687	-0.0026	0.3003	44.1681	-27.514	17.8438
6	6.6522	2.867	-0.6513	7.7174	-0.7128	5.3531	-0.1859	0.4985	-0.2615	-0.4359	0.1348	-0.3105	0.1401	0.0921	0.0339	0.1553	0.0288	0.0137	0.2231	-0.0242	0.1152	46.4744	-13.7315	-2.0943
7	4.5753	-0.4757	1.0256	8.5986	6.8286	5.8889	0.1128	0.346	0.3439	-0.655	0.0345	-0.2788	-0.5584	-0.0753	-0.1395	0.1841	0.0311	0.0273	0.1847	0.0483	0.1714	33.6915	-5.2506	6.3675
8	4.3809	-0.9514	-1.0203	2.1199	0.2661	3.6581	0.0028	0.1329	0.1783	-0.1572	0.1025	-0.327	-0.2076	0.1722	-0.0157	0.105	0.0171	-0.0038	0.1269	0.0242	0.1256	43.0711	-8.1352	10.6459
9	5.1814	0.6162	-0.4154	6.9095	-0.3416	4.2049	-0.0326	-0.0436	-0.0662	-0.1656	-0.1549	-0.8628	0.0126	0.5947	0.0368	0.1321	0.0222	-0.0092	0.2662	-0.0006	0.2505	53.0792	-12.4191	9.1243
10	5.5151	0.8071	-1.0795	9.1491	0.7944	8.1966	-0.1863	1.3093	0.3001	-0.8545	0.2697	-0.1038	-0.027	0.2363	-0.0616	0.2203	-0.0223	-0.0172	0.5243	0.0931	0.2323	24.4699	-8.3389	-3.0795
11	2.5286	0.2088	0.0203	5.0037	-2.7643	4.1034	-0.0442	0.2604	-0.0211	-0.2085	0.0697	0.0382	0.0535	-0.1554	-0.0591	0.1141	0.0123	-0.013	0.1813	-0.024	0.1391	14.2293	-23.1423	7.1564
12	4.0334	-0.839	-0.131	4.9242	6.4668	8.8187	0.0758	-0.4543	-0.385	0.534	-0.0074	-0.0722	0.7135	-0.1302	-0.0563	0.1946	-0.02	-0.0217	0.1996	0.0565	0.1733	24.7383	-20.6438	21.7269
13	2.1817	1.146	0.6533	4.3677	1.027	4.9295	-0.0019	-0.0526	-0.0607	0.2365	-0.0858	0.2584	0.1855	-0.599	0.0988	0.1358	-0.0156	-0.0175	0.1759	0.0295	0.1475	15.4084	-17.3736	18.0261
14	7.209	0.0207	-0.6657	7.9471	-4.8148	2.0422	0.1733	0.0805	-0.1448	0.1578	0.3084	0.7653	0.1329	-1.043	-0.4582	0.1783	-0.0231	-0.0166	0.2772	0.0137	0.2743	6.006	-20.0227	13.0137
15	2.0486	0.1422	1.1877	2.042	0.799	9.6694	-0.0107	0.3014	1.2558	0.4194	-0.0465	0.3921	-1.195	0.1467	0.0311	0.4087	-0.0127	0.0258	0.3174	0.044	0.5368	34.0979	10.3637	15.903
16	9.1761	1.3838	3.146	6.1994	-1.2463	2.0108	-0.2098	1.2062	0.2972	-0.6241	0.2036	-0.3533	-0.9406	0.7814	0.0078	0.3691	-0.0602	0.036	0.3351	-0.0239	0.4026	42.5443	9.054	17.4554
17	9.0274	-0.7025	-1.0749	4.8334	0.1306	6.4605	0.0332	-0.4366	-0.334	0.3996	-0.052	-0.2675	0.1051	0.384	-0.0097	0.208	0.0024	-0.0402	0.2647	-0.0164	0.1777	44.0511	-4.7862	38.2686
18	2.9604	0.8653	0.3452	4.1023	0.7581	2.8095	0.0376	-0.3404	-0.1194	0.2945	0.0062	-0.3211	0.1994	0.2213	-0.0353	0.171	0.0213	-0.0315	0.1953	0.0033	0.145	41.9717	-10.3895	26.6912

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 23 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 67 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 68 through 158 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 2 through 16 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 17 through 35 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 36 through 67 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 68 through 92 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 93 through 137 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 138 through 157 )	B
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 16 )	C
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 17 through 67 )	C
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 68 through 92 )	C
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 93 through 137 )	C
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 138 through 157 )	C
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 1 through 15 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 16 through 35 )	D
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 36 through 67 )	D
18	X-RAY DIFFRACTION	18	chain 'D' and (resid 68 through 157 )	D

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