PDB-3wv9: Guanylylpyridinol (GP)- and ATP-bound HcgE from Methanothermobact...

ID or keywords:

Entry

Database: PDB / ID: 3wv9

Title

Guanylylpyridinol (GP)- and ATP-bound HcgE from Methanothermobacter marburgensis

Components

Hmd co-occurring protein HcgE

Keywords

TRANSFERASE / E1 enzyme superfamily / UBA/THIF-type NAD/FAD binding fold / Adenylyltransferase / ATP binding

Function / homology

Uncharacterised conserved protein UCP006529, dinucleotide-utilising ThiF/HesA / THIF-type NAD/FAD binding fold / ThiF family / ATP binding / ADENOSINE-5'-TRIPHOSPHATE / Chem-FEG / Hmd co-occurring protein HcgE

Function and homology information

Biological species

Methanothermobacter marburgensis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

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

Citation

Journal: Nat Commun / Year: 2015
Title: Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor
Authors: Fujishiro, T. / Kahnt, J. / Ermler, U. / Shima, S.

History

Deposition	May 16, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3wv9.cif.gz	324.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3wv9_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	3wv9_full_validation.pdf.gz	2.5 MB	Display
Data in XML	3wv9_validation.xml.gz	37.3 KB	Display
Data in CIF	3wv9_validation.cif.gz	47.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wv/3wv9 ftp://data.pdbj.org/pub/pdb/validation_reports/wv/3wv9	HTTPS FTP

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Related structure data

Related structure data	3wv7C 3wv8C 3wvaC 3wvbC 3wvcC 1zudS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2g1m-d 5wl3-3 5wl3-1 5wl3-2 6agp-d 5l9b-1 3hqu-d 4izj-5 2ase-d 4urj-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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 - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #203 - Nov 2016 Aminopeptidase 1 and Autophagy similarity (2) #60 - Dec 2004 Ubiquitin similarity (2)

Deposited unit

A: Hmd co-occurring protein HcgE

B: Hmd co-occurring protein HcgE

C: Hmd co-occurring protein HcgE

D: Hmd co-occurring protein HcgE

hetero molecules

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

1

A: Hmd co-occurring protein HcgE

hetero molecules

defined by author
25.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Hmd co-occurring protein HcgE

hetero molecules

defined by author
24.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Hmd co-occurring protein HcgE

hetero molecules

defined by author
25.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: Hmd co-occurring protein HcgE

hetero molecules

defined by author
24.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

A: Hmd co-occurring protein HcgE

hetero molecules

A: Hmd co-occurring protein HcgE

hetero molecules

A: Hmd co-occurring protein HcgE

hetero molecules

defined by software
75.2 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

B: Hmd co-occurring protein HcgE

hetero molecules

B: Hmd co-occurring protein HcgE

hetero molecules

B: Hmd co-occurring protein HcgE

hetero molecules

defined by software
74.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

C: Hmd co-occurring protein HcgE

hetero molecules

C: Hmd co-occurring protein HcgE

hetero molecules

C: Hmd co-occurring protein HcgE

hetero molecules

defined by software
75.5 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

8

D: Hmd co-occurring protein HcgE

hetero molecules

D: Hmd co-occurring protein HcgE

hetero molecules

D: Hmd co-occurring protein HcgE

hetero molecules

defined by software
73 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.000, 85.000, 120.780
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	143
Space group name H-M	P3

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 7 - 211 / Label seq-ID: 7 - 211

Dom-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	A	A
2	1	B	B
1	2	A	A
2	2	C	C
1	3	A	A
2	3	D	D
1	4	B	B
2	4	C	C
1	5	B	B
2	5	D	D
1	6	C	C
2	6	D	D

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Hmd co-occurring protein HcgE Mass: 23738.266 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanothermobacter marburgensis (archaea) Strain: DSM 2133 / 14651 / NBRC 100331 / OCM 82 / Marburg / Gene: hcgE, MTBMA_c15310 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: D9PY12, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical	ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₅O₁₃P₃ / Comment: ATP, energy-carrying molecule*YM
#3: Chemical	ChemComp-FEG / 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine Mass: 542.393 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₉H₂₃N₆O₁₁P
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.65 Å³/Da / Density % sol: 53.64 %
Crystal grow	Method: vapor diffusion, sitting drop / pH: 4.6 Details: 35%(w/v)pentaerythritol ethoxylate 270, 200mM ammonium sulfate, 100mM sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature Room temperatureK

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

SLS

/ Beamline: X10SA / Wavelength: 1.008 Å

Detector

Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2013

Radiation

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

Radiation wavelength

Wavelength: 1.008 Å / Relative weight: 1

Reflection

Resolution: 2.75→50 Å / Num. obs: 25386 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.79 % / R_merge(I) obs: 0.105 / Net I/σ(I): 15

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.75-2.85		0.87	2.47	1	100
2.85-3		0.682	3.25	1	100
3-3.3		0.376	5.77	1	100
3.3-3.8		0.171	11.41	1	100
3.8-4.3		0.091	20.07	1	100
4.3-5.9		0.062	27.54	1	100
5.9-8		0.046	35.59	1	100
8-12		0.031	47.67	1	100
	12	0.031	53.27	1	98.1

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.8.0071	refinement
PDB_EXTRACT	3.14	data extraction
XDS		data scaling
XDS		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1ZUD

1zud

Resolution: 2.75→46.69 Å / Cor.coef. F_o:F_c: 0.96 / Cor.coef. F_o:F_c free: 0.931 / SU B: 18.764 / SU ML: 0.193 / Cross valid method: THROUGHOUT / ESU R Free: 0.31 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21389	1173	4.6 %	RANDOM
R_work	0.16538	-	-	-
obs	0.16759	24213	99.95 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 60.84 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.21 Å²	0.1 Å²	0 Å²
2-	-	0.21 Å²	0 Å²
3-	-	-	-0.67 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→46.69 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6220	0	280	15	6515

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.021	0.019	6600
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	2.499	2.027	8984
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.522	5	816
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.637	24.179	268
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.384	15	1108
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	23.024	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.15	0.2	1033
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.021	4821
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	3.975	4.185	3276
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	6.192	6.273	4088
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.523	4.423	3324
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	490	0.14
1	2	B	490	0.14
2	1	A	476	0.18
2	2	C	476	0.18
3	1	A	440	0.19
3	2	D	440	0.19
4	1	B	464	0.2
4	2	C	464	0.2
5	1	B	436	0.19
5	2	D	436	0.19
6	1	C	418	0.22
6	2	D	418	0.22

LS refinement shell

Resolution: 2.75→2.821 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.219	90	-
R_work	0.161	1781	-
obs	-	-	100 %

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	0.7053	-0.4969	-0.4747	0.4437	0.3446	0.3213	-0.0701	-0.0162	-0.0091	-0.0814	0.0706	0.0513	0.0316	0.0216	-0.0005	0.2226	-0.007	-0.0469	0.2324	-0.0114	0.1609	28.1464	15.7258	-39.1967
2	2.4548	0.5172	-0.1058	1.4904	0.1913	0.0459	0.0331	-0.1315	-0.1104	-0.0191	-0.0576	0.0035	-0.0439	0.0044	0.0245	0.2314	-0.0192	0.0108	0.22	0.007	0.1335	40.5006	10.0604	-29.0208
3	0.2187	-0.1157	0.1273	0.6691	0.0081	0.1147	0.0415	0.0749	-0.1225	-0.0531	0.0142	0.0983	-0.049	0.0357	-0.0558	0.2083	-0.0225	0.0049	0.2301	-0.0951	0.1341	35.6959	4.5799	-45.6814
4	0.4952	-0.1551	0.2511	0.4619	-0.2128	0.1729	-0.0038	0.0346	-0.0616	0.0619	0.0087	-0.0401	-0.0218	-0.0084	-0.0049	0.2082	0.0085	0.0309	0.2333	-0.0076	0.1538	47.4833	10.9666	26.9371
5	0.1736	-0.0727	0.1627	1.5516	-0.0446	0.2211	-0.0106	0.0379	-0.0904	-0.0579	0.0621	-0.3131	-0.0127	-0.0675	-0.0515	0.1922	0.0149	0.0618	0.2007	-0.0524	0.207	58.6213	4.9118	18.5465
6	0.7505	-0.037	0.2764	0.1833	-0.0596	0.1193	0.0283	0.1533	-0.046	-0.0629	-0.0077	0.0056	-0.0071	0.042	-0.0206	0.2795	-0.0219	0.0852	0.2416	-0.076	0.0783	55.8639	11.9267	8.3276
7	0.5409	-0.0146	-0.1846	0.0249	0.0451	0.1732	-0.0596	-0.0614	-0.0488	-0.0022	-0.0045	-0.0165	0.0003	-0.0195	0.0641	0.1936	-0.0101	-0.0518	0.225	0.0582	0.1851	19.373	-1.2274	-17.0126
8	0.7026	0.0268	-1.5304	0.0021	-0.0602	3.3599	0.0583	-0.1078	-0.0056	-0.0092	-0.0067	0.0111	-0.1056	0.1792	-0.0517	0.1465	-0.0208	-0.1336	0.2166	0.1048	0.2074	25.2452	-5.48	-2.1307
9	0.9644	-0.8305	-0.4268	0.8741	0.4687	0.2538	-0.306	-0.5482	-0.1039	0.2434	0.2414	0.1652	0.1364	0.1046	0.0645	0.3294	0.0224	-0.0987	0.6578	0.0324	0.1151	12.795	-2.94	-8.3845
10	1.6282	2.2778	1.7826	3.1934	2.4884	1.9564	-0.1073	0.0671	0.0325	-0.1816	0.0947	0.0765	-0.0885	0.0776	0.0127	0.2876	-0.0189	-0.0505	0.1862	-0.0048	0.214	28.6467	-0.8466	46.6343
11	0.7078	0.605	-0.3407	1.1259	-0.3576	0.1815	0.0198	-0.0416	0.0157	0.0892	-0.0659	-0.1033	-0.0094	-0.0023	0.0462	0.21	-0.0167	-0.0613	0.2053	-0.0431	0.1856	51.7769	-9.2927	37.8112
12	0.4368	-0.0731	0.3137	0.1566	-0.4102	1.1117	0.0281	-0.397	0.0895	-0.016	-0.0535	-0.0011	0.0434	-0.0075	0.0254	0.2541	-0.0267	-0.1073	0.4478	-0.0913	0.0713	57.1172	-10.3892	54.1926

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	7 - 41
2	X-RAY DIFFRACTION	2	A	42 - 72
3	X-RAY DIFFRACTION	3	A	73 - 211
4	X-RAY DIFFRACTION	4	B	7 - 82
5	X-RAY DIFFRACTION	5	B	83 - 144
6	X-RAY DIFFRACTION	6	B	145 - 211
7	X-RAY DIFFRACTION	7	C	7 - 163
8	X-RAY DIFFRACTION	8	C	164 - 179
9	X-RAY DIFFRACTION	9	C	180 - 211
10	X-RAY DIFFRACTION	10	D	7 - 12
11	X-RAY DIFFRACTION	11	D	13 - 114
12	X-RAY DIFFRACTION	12	D	115 - 211

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