PDB-6exi: NAD-free crystal structure of S-adenosyl-L-homocysteine hydrolase...

ID or keywords:

Entry

Database: PDB / ID: 6exi

Title

NAD-free crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii complexed with adenosine

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / NAD / adnosine / hydorolase / SAHase / S-adenosyl-L-homocysteine / SAH / S-adenosyl-L-methionine / SAM / methylation / methyltransferases

Function / homology

Function and homology information

L-homocysteine biosynthetic process / adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / cytosol
Similarity search - Function

Biological species

Bradyrhizobium elkanii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.918 Å

Authors

Manszewski, T. / Jaskolski, M.

Citation

Journal: Front Microbiol / Year: 2018
Title: S-Adenosyl-L-Homocysteine Hydrolase Inhibition by a Synthetic Nicotinamide Cofactor Biomimetic.
Authors: Kailing, L.L. / Bertinetti, D. / Paul, C.E. / Manszewski, T. / Jaskolski, M. / Herberg, F.W. / Pavlidis, I.V.

History

Deposition	Nov 8, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 19, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	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 / pdbx_struct_conn_angle / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6exi.cif.gz	743.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6exi.ent.gz	615.4 KB	Display	PDB format
PDBx/mmJSON format	6exi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6exi_validation.pdf.gz	2.7 MB	Display	wwPDB validaton report
Full document	6exi_full_validation.pdf.gz	2.8 MB	Display
Data in XML	6exi_validation.xml.gz	77.7 KB	Display
Data in CIF	6exi_validation.cif.gz	115.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ex/6exi ftp://data.pdbj.org/pub/pdb/validation_reports/ex/6exi	HTTPS FTP

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Related structure data

Related structure data	5m66S 4lvc 5m55 5m56 5m57 5m5k 5tov 5tow S: Starting model for refinement
Similar structure data	3glq-1 3n58-d 5m66-d 5m5k-d 2ziz-d 2zj0-d 3dhy-d 5v96-d 5m67-d 3onf-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18150/repod.1173852 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	90.635, 124.360, 92.721
Angle α, β, γ (deg.)	90.00, 103.71, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Adenosylhomocysteinase / BeSAHase / S-adenosyl-L-homocysteine hydrolase / SAHase Mass: 52737.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium elkanii (bacteria) / Gene: ahcY / Production host: Escherichia coli (E. coli) / References: UniProt: A0A087WNH6, adenosylhomocysteinase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1382 / 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: 2.44 Å³/Da / Density % sol: 48.9 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.3 M sodium acetate, 16% PEG 400, 0.1 M Tris pH 8.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 9, 2017
Radiation	Monochromator: Sagittally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.92→47.083 Å / Num. obs: 151344 / % possible obs: 99.3 % / Redundancy: 5.7 % / B_iso Wilson estimate: 28.38 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.124 / R_rim(I) all: 0.137 / Net I/av σ(I): 10.12 / Net I/σ(I): 10.12
Reflection shell	Resolution: 1.92→2.03 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 24151 / CC_1/2: 0.794 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5m66

5m66

Resolution: 1.918→47.083 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.75 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2175	1011	0.67 %	Random
R_work	0.1726	-	-	-
obs	0.1729	151320	99.31 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.918→47.083 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14484	0	163	1382	16029

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.013	15041
X-RAY DIFFRACTION	f_angle_d	1.178	20357
X-RAY DIFFRACTION	f_dihedral_angle_d	16.602	9020
X-RAY DIFFRACTION	f_chiral_restr	0.068	2278
X-RAY DIFFRACTION	f_plane_restr	0.007	2610

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9183-2.0194	0.2826	142	0.2385	21166	X-RAY DIFFRACTION	98
2.0194-2.1459	0.235	144	0.2064	21482	X-RAY DIFFRACTION	100
2.1459-2.3116	0.2344	145	0.1905	21444	X-RAY DIFFRACTION	99
2.3116-2.5442	0.2196	144	0.1849	21514	X-RAY DIFFRACTION	100
2.5442-2.9123	0.2204	145	0.1882	21481	X-RAY DIFFRACTION	99
2.9123-3.669	0.2264	145	0.169	21535	X-RAY DIFFRACTION	99
3.669-47.0967	0.1852	146	0.137	21687	X-RAY DIFFRACTION	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	1.1252	0.1025	0.4556	0.9229	0.3094	1.0784	-0.0491	-0.0101	-0.0228	-0.0009	0.0965	-0.0581	-0.0012	0.0012	-0.0481	0.157	0.0181	0.0002	0.2042	-0.0103	0.1832	-24.1044	72.0664	11.6193
2	1.6568	0.0581	-0.3675	0.7196	-0.1029	0.8691	-0.0487	0.0845	-0.1752	-0.0537	-0.0056	0.0222	0.0819	-0.2013	0.0549	0.2318	0.0177	-0.0212	0.2633	-0.0299	0.2018	-10.9733	51.8122	25.5993
3	2.2328	0.5561	1.0401	-0.1266	-0.1712	0.8355	-0.1556	0.186	0.2192	-0.0639	0.0074	-0.0585	-0.1037	0.104	0.1544	0.3042	0.0152	-0.005	0.213	0.0062	0.2757	-1.6601	82.7171	14.7083
4	1.0879	0.2906	-0.4073	1.4133	-0.2242	0.8796	-0.0604	0.0211	-0.028	-0.0239	-0.0014	0.0406	-0.0135	-0.0037	0.0569	0.1706	0.0127	-0.0092	0.1719	-0.0022	0.2114	36.14	66.7943	10.7557
5	4.6303	3.1211	-4.18	2.6428	-2.3637	4.5423	0.2501	0.1502	0.9244	0.2274	0.2225	0.6591	-0.3227	-0.3154	-0.4989	0.2622	0.0565	-0.0117	0.3113	-0.0007	0.4492	19.6089	73.3134	6.5455
6	1.9993	-0.1639	0.5903	0.8008	-0.0214	1.054	-0.0026	-0.0285	0.11	0.0145	-0.0473	-0.0441	-0.1512	0.0332	0.0538	0.2501	-0.0047	0.0275	0.173	0.018	0.1914	18.212	77.1012	32.5989
7	0.8013	0.2152	0.0852	-0.2899	-0.2012	1.1147	-0.1013	0.1395	-0.0082	-0.1068	-0.003	0.0422	-0.1085	-0.1018	0.1083	0.2548	0.0401	-0.011	0.223	-0.0031	0.2694	16.2555	62.4481	14.7885
8	1.5353	-0.3102	-0.3208	0.8964	0.3614	1.56	0.0595	-0.0556	-0.0257	-0.0058	-0.0363	0.0287	-0.0529	-0.2611	-0.0244	0.177	-0.0105	-0.001	0.3309	0.0167	0.2268	-25.7651	52.5369	58.958
9	4.3495	-3.1438	-1.2184	4.2663	0.8608	2.4439	0.0846	-0.3786	0.0855	0.1108	0.0198	0.0886	-0.1072	-0.2591	-0.1011	0.198	-0.047	-0.0283	0.4214	-0.0299	0.1831	-27.2575	59.7272	72.6759
10	0.1087	0.1478	-0.7081	0.6121	-1.8881	4.6618	-0.0403	-0.1245	-0.0668	0.0856	-0.1289	-0.1601	-0.2536	0.0216	0.1862	0.2246	-0.0272	-0.0165	0.3124	-0.0084	0.2776	-9.741	58.2109	59.0762
11	2.0574	-0.2722	1.14	0.791	-0.3198	0.969	-0.0872	-0.366	0.1705	0.0723	-0.0074	0.054	-0.1766	-0.2611	0.0801	0.2422	0.0301	0.0059	0.2938	-0.048	0.1904	-7.2878	75.1325	49.3219
12	0.4269	-0.1066	0.3258	1.3513	-0.7299	1.2746	-0.0088	-0.0899	-0.0267	0.1074	-0.0223	-0.1016	-0.0783	-0.1424	0.0358	0.1987	0.0012	0.0043	0.3004	-0.0022	0.2427	-13.5234	56.5462	55.7888
13	1.361	-0.7192	-0.3151	1.8561	0.2563	1.5221	-0.0476	-0.2826	-0.3994	0.2646	-0.0249	0.039	0.2755	-0.036	0.0632	0.2603	-0.0167	0.0329	0.3007	0.1242	0.3336	7.5582	39.4309	54.0695
14	0.9907	0.1166	0.0508	1.4419	-1.1024	1.5768	-0.0846	0.1044	-0.0739	-0.1247	-0.0359	-0.1914	0.1564	0.0255	0.1142	0.2065	-0.0201	0.0129	0.1644	-0.023	0.2051	35.8493	55.7433	62.3642
15	0.3837	-0.4188	0.9743	-0.0468	-0.5661	3.8504	-0.0251	-0.1231	-0.0444	-0.0392	0.0111	0.0272	0.3282	-0.5231	-0.0014	0.2673	-0.0609	-0.0015	0.2473	0.0147	0.2807	19.5363	53.2807	57.7574
16	1.0471	0.485	-0.3799	1.0554	-0.3498	1.1328	-0.0734	-0.0872	-0.3014	-0.0471	-0.0562	-0.1647	0.181	0.0876	0.1156	0.2318	0.0195	0.0114	0.1907	0.0711	0.2971	19.2689	44.964	39.3541
17	1.2261	-0.9131	0.8042	0.5909	-0.1233	1.2857	-0.2147	-0.2091	0.0307	0.1786	0.1104	0.0473	-0.0739	-0.3787	0.1016	0.2498	0.0026	0.004	0.2903	-0.0153	0.1982	11.8001	67.0121	66.2983

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 230 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 231 through 393 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 394 through 473 )
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 4 through 198 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 199 through 230 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 231 through 361 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 362 through 473 )
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 6 through 162 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 163 through 198 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 199 through 248 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 249 through 361 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 362 through 439 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 440 through 473 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 6 through 198 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 199 through 248 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 249 through 393 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 394 through 473 )

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