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

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Open data

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Basic information

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

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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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

Summary document	5d4v_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	5d4v_full_validation.pdf.gz	1.9 MB	Display
Data in XML	5d4v_validation.xml.gz	50.3 KB	Display
Data in CIF	5d4v_validation.cif.gz	73.2 KB	Display
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

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Assembly

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)

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)

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

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Components

#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 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.: 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 Mass: 18.015 Da / Num. of mol.: 937 / Source method: isolated from a natural source / Formula: H₂O

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Experimental details

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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: _

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 /

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Processing