PDB-8cfg: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. ...

ID or keywords:

Entry

Database: PDB / ID: 8cfg

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment C04

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / Fragment screening / protein-ligand complex / drug discovery / SAM-DEPENDENT METHYLATION REACTIONS / SAHase / AHCY

Function / homology

Function and homology information

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

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.73 Å

Authors

Malecki, P.H. / Gawel, M. / Stepniewska, M. / Brzezinski, K.

Funding support

Poland, 1items

Citation

Journal: To be published
Title: Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with fragment F2X-Entry C04
Authors: Malecki, P.H. / Gawel, M. / Stepniewska, M. / Brzezinski, K.

History

Deposition	Feb 3, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 21, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8cfg.cif.gz	757.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8cfg.ent.gz	627 KB	Display	PDB format
PDBx/mmJSON format	8cfg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cfg_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	8cfg_full_validation.pdf.gz	2.8 MB	Display
Data in XML	8cfg_validation.xml.gz	81.6 KB	Display
Data in CIF	8cfg_validation.cif.gz	120.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfg ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfg	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases 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
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	73.940, 132.800, 98.780
Angle α, β, γ (deg.)	90.00, 101.13, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 51735.031 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: ahcY, sahH, PA0432 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase

Mass: 51735.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa PAO1 (bacteria) / Strain: PAO1 / Gene: ahcY, sahH, PA0432 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 8 types, 1613 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Chemical	ChemComp-ADE / ADENINE Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₅N₅
#4: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#5: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-R8S / 2-hydrazinyl-4-methoxypyrimidine Mass: 140.143 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₅H₈N₄O / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1575 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.3 Å³/Da / Density % sol: 46.51 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 50 mM KH2PO4, 20% (w/v) PEG8000, 20% (v/v) glycerol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.2 / Wavelength: 0.9184 Å

Detector

Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 27, 2021

Radiation

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

Radiation wavelength

Wavelength: 0.9184 Å / Relative weight: 1

Reflection

Resolution: 1.73→41.59 Å / Num. obs: 189489 / % possible obs: 97.2 % / Redundancy: 4.72 % / CC_1/2: 0.997 / R_merge(I) obs: 0.13 / R_rim(I) all: 0.147 / Net I/σ(I): 8.72

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.73-1.83	1.707	29828	0.425	1.913	1
1.83-1.96	1.014	28565	0.648	1.137	1
1.96-2.12	0.578	26777	0.826	0.651	1
2.12-2.32	0.327	24672	0.922	0.372	1
2.32-2.59	0.204	22428	0.967	0.231	1
2.59-2.99	0.127	19899	0.989	0.143	1
2.99-3.66	0.069	16854	0.996	0.078	1
3.66-5.15	0.039	13077	0.998	0.045	1
5.15-41.59	0.033	7389	0.999	0.037	1

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2-4158	refinement
XDS		data scaling
XDS		data reduction
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.73→37.12 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.57 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2012	2100	1.11 %
R_work	0.1615	-	-
obs	0.1619	189426	97.2 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.73→37.12 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14228	0	378	1575	16181

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	15032
X-RAY DIFFRACTION	f_angle_d	0.807	20391
X-RAY DIFFRACTION	f_dihedral_angle_d	13.634	5576
X-RAY DIFFRACTION	f_chiral_restr	0.054	2267
X-RAY DIFFRACTION	f_plane_restr	0.006	2695

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 (%)
1.73-1.77	0.3917	134	0.3344	11926	X-RAY DIFFRACTION	93
1.77-1.81	0.3269	137	0.3077	12270	X-RAY DIFFRACTION	96
1.81-1.86	0.3358	139	0.2714	12408	X-RAY DIFFRACTION	97
1.86-1.92	0.2641	139	0.2434	12398	X-RAY DIFFRACTION	97
1.92-1.98	0.2645	139	0.2229	12414	X-RAY DIFFRACTION	97
1.98-2.05	0.2615	140	0.2052	12462	X-RAY DIFFRACTION	97
2.05-2.13	0.2195	139	0.182	12441	X-RAY DIFFRACTION	97
2.13-2.23	0.2261	140	0.1681	12494	X-RAY DIFFRACTION	97
2.23-2.35	0.2017	141	0.1573	12552	X-RAY DIFFRACTION	98
2.35-2.49	0.2183	141	0.1539	12560	X-RAY DIFFRACTION	98
2.49-2.68	0.211	141	0.1513	12608	X-RAY DIFFRACTION	98
2.69-2.96	0.1798	142	0.1427	12656	X-RAY DIFFRACTION	98
2.96-3.38	0.1695	142	0.1413	12651	X-RAY DIFFRACTION	98
3.38-4.26	0.1599	142	0.1219	12698	X-RAY DIFFRACTION	99
4.26-37.12	0.1712	144	0.143	12788	X-RAY DIFFRACTION	98

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	2.2039	-0.518	-0.9223	1.0452	1.4753	2.334	0.0464	0.0033	0.1918	-0.1373	0.0033	-0.0623	-0.2109	-0.0043	-0.0704	0.2817	-0.0051	-0.0261	0.1211	0.0248	0.2498	-4.1498	62.9023	-16.6795
2	1.8182	0.1719	-0.406	1.0936	0.3132	2.0319	0.0167	0.0109	0.2217	-0.1125	0.0074	0.0374	-0.2325	-0.0598	-0.017	0.2326	0.0164	-0.0299	0.125	-0.0207	0.2172	-12.7739	61.0252	-17.5738
3	2.6167	-2.7337	1.1156	5.2253	-3.9611	8.4406	-0.1273	-0.1409	0.1358	0.1899	0.2221	0.5019	-0.475	-0.7435	-0.1359	0.2179	0.049	-0.0363	0.2582	-0.0642	0.3043	-25.414	62.9307	-13.6887
4	6.0746	-0.6133	-2.3415	3.3043	0.9671	4.8931	0.0183	0.1035	0.2009	-0.0766	-0.1176	0.4304	-0.1382	-0.5539	0.1003	0.269	0.023	-0.0912	0.28	-0.0479	0.2478	-26.581	58.1937	-24.2665
5	1.0858	-0.9779	0.8393	1.3558	-0.7353	1.8548	-0.021	0.0858	-0.0688	-0.1599	-0.0485	0.173	-0.086	-0.1607	0.0685	0.2588	-0.0179	-0.0264	0.2013	-0.0255	0.2577	-15.5601	44.6926	-25.3923
6	0.7555	0.1215	0.3012	0.821	0.5561	1.9447	0.0218	-0.08	-0.0434	0.0387	-0.0375	0.1326	0.0217	-0.1895	0.0173	0.1385	0.0043	-0.0003	0.1565	0.0081	0.1993	-15.5565	28.8774	-13.9471
7	2.2423	1.192	-0.457	4.1496	-1.9559	3.069	0.0393	-0.3068	-0.019	0.2667	-0.0704	0.1521	-0.0107	-0.2724	-0.0154	0.1413	0.0049	0.0046	0.197	-0.0325	0.139	-14.5915	35.6261	-2.6486
8	2.0037	0.2425	-1.3762	2.659	0.3791	1.361	0.005	0.61	0.2229	-0.5125	-0.0727	0.4147	-0.1845	-0.4721	0.0272	0.363	0.0495	-0.0885	0.302	0.0079	0.2395	-18.4864	58.4598	-34.8464
9	2.0402	0.113	-0.3978	1.3039	0.6781	1.2206	0.0991	0.2704	0.1716	-0.305	-0.0895	-0.0299	-0.3113	-0.0332	-0.0197	0.3531	0.014	-0.0073	0.1973	0.0521	0.1911	-1.2519	47.095	-44.5622
10	3.2915	-0.579	2.6239	3.3374	-1.7543	2.8411	-1.4764	0.1672	0.7134	-1.0314	0.9245	1.9962	-0.5789	0.1968	0.5484	0.214	-0.0101	-0.0015	0.1667	0.055	0.281	-9.5739	49.5018	-19.0813
11	3.2189	1.0067	1.2109	4.1237	2.0921	1.7837	-0.0653	-0.2528	0.2628	0.1215	-0.0532	0.1776	-0.1527	-0.1962	0.1097	0.241	0.0577	0.0204	0.2606	0.0178	0.169	-1.1637	39.2543	11.8419
12	2.7085	0.2736	2.7394	2.3554	-0.9275	6.2711	0.1476	-0.3008	-0.2329	0.2042	0.1014	0.0416	0.3999	-0.2132	-0.2321	0.2031	0.0677	0.0318	0.2251	-0.01	0.1507	7.8156	24.7977	13.3065
13	0.853	-0.2784	0.5455	1.8592	-0.5797	2.396	-0.1339	-0.1883	0.1412	0.263	0.0963	-0.1053	-0.2312	0.0266	0.0547	0.1856	0.0479	-0.0257	0.1798	-0.0498	0.152	11.3251	39.4435	14.0894
14	3.3674	-0.2842	2.3183	3.1651	-0.9938	6.3449	0.0006	-0.1717	0.0829	0.2016	0.1073	-0.2341	0.0343	0.2631	-0.1068	0.1361	0.0464	-0.0269	0.2205	-0.0562	0.168	24.1263	33.1813	14.0568
15	1.5926	-1.3813	1.6915	1.533	-1.0302	2.1916	0.0431	0.0274	0.0303	-0.0556	0.0105	-0.058	0.1336	0.1559	-0.0355	0.1709	-0.023	0.0194	0.2332	-0.0095	0.1839	18.2663	30.9792	-2.232
16	0.8518	-0.4447	-0.1151	1.155	0.3597	0.597	0.0159	0.0413	0.1871	-0.0953	0.0361	-0.2142	-0.1434	0.1277	-0.0537	0.1967	-0.0592	0.0163	0.1992	0.0049	0.2197	19.2765	43.8751	-16.8037
17	2.2788	0.5663	-0.555	4.675	-1.7302	2.7003	0.0488	0.0455	0.3735	0.0684	0.0544	-0.2185	-0.4435	0.0614	-0.0614	0.1906	-0.0212	0.0205	0.142	-0.0293	0.2113	12.7943	53.3962	-10.2823
18	1.5555	0.7968	1.0501	0.5152	0.5846	2.8762	0.0358	-0.0688	-0.2275	0.2112	0.0833	-0.1546	0.2409	0.209	-0.147	0.2117	0.0376	-0.0165	0.14	-0.0096	0.1707	20.1878	20.8834	11.3246
19	2.8135	-0.6655	-0.0857	2.5568	0.1225	1.8042	0.0412	-0.1836	-0.2199	0.0975	0.0088	0.0264	0.2092	0.0348	-0.0462	0.1694	-0.014	-0.0205	0.1522	0.0402	0.1567	10.9734	8.3224	-5.3511
20	7.1697	-5.8941	-1.1873	8.4655	1.731	2.898	-0.3147	-0.0835	-0.3753	-0.4683	-0.0219	0.3551	-0.6826	0.2058	0.3417	0.2533	-0.0242	-0.0713	0.1806	0.0103	0.2709	9.4727	34.4937	0.6753
21	1.8555	0.3458	0.1405	1.1035	-0.5015	1.7761	0.028	0.2523	-0.2392	-0.1501	0.0802	-0.1616	0.2728	0.1326	-0.1101	0.2113	0.0398	0.0176	0.2601	-0.088	0.2505	31.2959	6.9072	-38.3129
22	4.3781	-0.6431	0.9118	3.869	1.1097	4.3526	0.1165	0.1195	-0.8751	-0.0357	0.0384	-0.0597	0.87	-0.0447	-0.1527	0.4574	0.0398	-0.0706	0.2598	-0.061	0.4487	31.6855	-7.3492	-29.8532
23	2.3832	-0.5323	1.1767	0.6607	-0.043	2.1165	0.1503	-0.1948	-0.3385	0.1144	0.0364	-0.0794	0.2579	0.1235	-0.1493	0.2153	-0.0163	-0.0108	0.2022	0.01	0.2546	25.3102	5.3685	-21.6459
24	0.6035	0.0245	0.2408	0.6343	0.4871	2.1868	0.0614	0.0135	-0.2069	0.0212	-0.0129	0.0331	0.2696	-0.0651	-0.0425	0.1772	0.0032	-0.0217	0.1338	0.0051	0.2317	2.1954	5.6428	-22.0556
25	2.5665	1.0241	-0.7857	2.8896	-0.2319	2.2704	0.0242	0.2009	-0.5642	-0.0978	0.0308	-0.0006	0.4731	-0.1175	-0.0652	0.271	0.0112	-0.054	0.1611	-0.037	0.2398	2.2168	-0.1952	-33.9019
26	0.9337	-0.3981	-0.1509	1.4806	1.0616	1.8063	0.0113	-0.0975	-0.0692	0.2052	0.1672	-0.3448	0.2104	0.3433	-0.1354	0.1469	-0.0053	-0.0264	0.2809	-0.0279	0.2698	34.9387	19.1268	-17.8278
27	1.9972	1.9958	1.9983	2.0013	2.002	2.0033	-0.1352	-1.5799	-0.0041	-0.5094	-0.1327	0.9206	0.1219	1.7099	0.3047	0.2408	0.0237	-0.0773	0.4001	-0.0581	0.3343	21.8734	9.4935	-31.3678
28	0.8438	-0.2313	0.4974	0.5112	-0.1234	0.91	0.0966	0.1894	-0.0664	-0.2032	-0.0755	0.0523	0.0446	0.0611	-0.0189	0.2476	0.0422	-0.0385	0.2528	-0.0522	0.1907	-8.0457	17.6517	-55.9489
29	0.5423	-0.0464	0.1664	0.4821	0.0928	0.5522	0.0442	0.1763	0.0227	-0.1485	-0.0422	-0.0282	-0.1047	0.0716	-0.0012	0.2016	0.0102	0.0028	0.1781	0.0036	0.1263	1.6606	30.3522	-44.7543
30	2.5826	2.1301	2.5855	3.0281	1.7914	2.7723	-0.3893	-0.3924	-0.0136	-0.4983	0.5603	1.2727	0.0983	1.1533	-0.1821	0.2275	0.0544	-0.0423	0.3361	-0.0478	0.2533	-2.913	19.1015	-47.8911

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 6 through 45 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 112 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 113 through 134 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 135 through 165 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 166 through 215 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 216 through 350 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 351 through 383 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 384 through 424 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 425 through 469 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 502 through 502 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 9 through 34 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 35 through 63 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 64 through 134 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 135 through 165 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 166 through 215 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 216 through 350 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 351 through 383 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 384 through 424 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 425 through 469 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 503 through 503 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 10 through 112 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 113 through 150 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 151 through 215 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 216 through 350 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 351 through 383 )
26	X-RAY DIFFRACTION	26	chain 'C' and (resid 384 through 469 )
27	X-RAY DIFFRACTION	27	chain 'C' and (resid 502 through 502 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 8 through 215 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 216 through 469 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 502 through 502 )

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