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

ID or keywords:

Entry

Database: PDB / ID: 8cfj

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment D10

Components

Adenosylhomocysteinase

Keywords

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

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

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.64 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 D10
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	8cfj.cif.gz	759.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8cfj.ent.gz	628.2 KB	Display	PDB format
PDBx/mmJSON format	8cfj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cfj_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8cfj_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8cfj_validation.xml.gz	81 KB	Display
Data in CIF	8cfj_validation.cif.gz	120.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfj ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfj	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)	74.110, 132.720, 99.030
Angle α, β, γ (deg.)	90.00, 101.41, 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, 1599 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-R9J / 2-methyl-N-(4-methylphenyl)-L-alanine Mass: 193.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₅NO₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#7: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO₄
#8: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#9: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1564 / 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: 2.31 Å³/Da / Density % sol: 46.68 %
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: 1.64→36.47 Å / Num. obs: 222867 / % possible obs: 97.2 % / Redundancy: 4.69 % / CC_1/2: 0.998 / R_merge(I) obs: 0.106 / R_rim(I) all: 0.12 / Net I/σ(I): 9.81

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.64-1.74	1.868	35144	0.345	2.114	1
1.74-1.86	1.207	33528	0.584	1.351	1
1.86-2.01	0.654	31362	0.817	0.733	1
2.01-2.2	0.351	29005	0.928	0.396	1
2.2-2.46	0.196	26365	0.974	0.222	1
2.46-2.83	0.113	23404	0.991	0.127	1
2.83-3.46	0.061	19863	0.997	0.068	1
3.46-4.88	0.032	15478	0.999	0.037	1
4.88-36.47	0.026	8718	0.999	0.029	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: 1.64→27.39 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.66 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2014	2339	1.05 %
R_work	0.1677	-	-
obs	0.168	222767	97.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.64→27.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14228	0	347	1564	16139

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	15013
X-RAY DIFFRACTION	f_angle_d	0.785	20377
X-RAY DIFFRACTION	f_dihedral_angle_d	14.11	5589
X-RAY DIFFRACTION	f_chiral_restr	0.053	2270
X-RAY DIFFRACTION	f_plane_restr	0.006	2693

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 (%)
1.64-1.67	0.3604	132	0.3465	12401	X-RAY DIFFRACTION	93
1.67-1.71	0.336	136	0.3312	12760	X-RAY DIFFRACTION	96
1.71-1.75	0.3222	136	0.3038	12816	X-RAY DIFFRACTION	96
1.75-1.79	0.2695	136	0.2809	12819	X-RAY DIFFRACTION	96
1.79-1.84	0.2777	136	0.2605	12829	X-RAY DIFFRACTION	97
1.84-1.89	0.2919	136	0.2425	12908	X-RAY DIFFRACTION	97
1.89-1.96	0.2429	137	0.217	12917	X-RAY DIFFRACTION	97
1.96-2.03	0.2251	138	0.197	12954	X-RAY DIFFRACTION	97
2.03-2.11	0.2364	138	0.1832	12996	X-RAY DIFFRACTION	97
2.11-2.2	0.2306	137	0.1688	12965	X-RAY DIFFRACTION	97
2.2-2.32	0.2056	138	0.1652	12997	X-RAY DIFFRACTION	97
2.32-2.46	0.1829	139	0.1581	13052	X-RAY DIFFRACTION	98
2.46-2.65	0.1946	138	0.1604	13067	X-RAY DIFFRACTION	98
2.65-2.92	0.1852	140	0.1532	13171	X-RAY DIFFRACTION	99
2.92-3.34	0.2128	140	0.1494	13161	X-RAY DIFFRACTION	98
3.34-4.21	0.1615	140	0.1264	13224	X-RAY DIFFRACTION	99
4.21-27.39	0.1616	142	0.1429	13391	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	1.9533	-0.4467	-0.571	1.1783	1.3852	1.6628	0.0367	0.0151	0.2753	-0.1698	-0.012	-0.1093	-0.2455	-0.0532	-0.0561	0.3275	0.0068	-0.0378	0.1532	0.018	0.2892	-4.1665	62.8809	-16.6569
2	1.8726	-0.0436	-0.466	1.296	0.4636	2.2545	0.001	-0.0047	0.2373	-0.1194	0.0059	0.04	-0.209	-0.1116	0.0139	0.2575	0.015	-0.0371	0.1444	-0.0219	0.2482	-12.7577	61.0037	-17.5771
3	2.9942	-2.2769	1.0667	4.3921	-3.0143	8.4573	-0.0827	-0.1896	0.1201	0.1817	0.1136	0.5772	-0.5846	-0.8749	-0.0738	0.2536	0.0457	-0.0317	0.3014	-0.0894	0.3453	-25.4073	63.0482	-13.7496
4	5.8068	-0.8315	-1.6165	3.6961	0.545	4.7803	-0.0228	0.0785	0.0816	0.0182	-0.1072	0.4685	0.0958	-0.7911	0.1091	0.326	-0.0067	-0.0933	0.3908	-0.0547	0.3154	-26.5354	58.1964	-24.3528
5	0.9021	-0.9134	0.9838	1.5707	-0.7424	2.013	-0.0094	0.0224	-0.1153	-0.2579	0.0205	0.289	-0.0762	-0.2573	-0.0171	0.2877	-0.0242	-0.0292	0.2513	-0.0179	0.291	-15.8224	44.8089	-25.6126
6	0.7189	0.1738	0.3624	0.8171	0.5701	1.9019	0.0202	-0.1042	-0.0286	0.0569	-0.0451	0.1714	-0.0369	-0.2526	0.0316	0.1584	0.0117	0.0105	0.1808	0.0064	0.2152	-15.4682	28.7965	-14.0004
7	2.2573	1.3503	-0.4654	4.0735	-1.7425	3.5688	0.0693	-0.3676	-0.0155	0.3662	-0.1201	0.1779	-0.0709	-0.3443	-0.0025	0.1655	0.0089	0.0173	0.2314	-0.0187	0.1668	-14.6635	35.5735	-2.7116
8	2.0817	0.2608	-1.6496	3.4372	0.9345	1.8317	0.0127	0.722	0.1573	-0.5033	-0.179	0.4881	-0.2022	-0.6933	0.1207	0.4097	0.0445	-0.0872	0.407	-0.0073	0.2577	-18.4923	58.5357	-34.8719
9	2.0173	0.1044	-0.0742	1.8284	0.5793	1.1743	0.0952	0.2963	0.2176	-0.2906	-0.108	-0.0086	-0.4034	0.0233	0.0122	0.3497	0.0073	0.0015	0.2077	0.0563	0.2014	-1.2016	47.1271	-44.6571
10	2.1441	-2.8438	2.6007	4.3877	-4.0803	3.8009	-1.4543	0.5159	0.6896	-0.7329	1.1317	1.8181	-0.6692	0.2203	0.3305	0.2552	-0.0468	-0.0227	0.1542	0.059	0.2586	-9.5793	49.4482	-19.0655
11	2.6726	0.6742	0.9466	3.473	1.4169	1.8156	-0.1125	-0.324	0.2687	0.2064	0.0134	0.1159	-0.1672	-0.1896	0.1025	0.2711	0.0738	0.0101	0.2943	0.0007	0.1953	-1.2705	39.1686	11.842
12	2.2698	0.0716	2.0144	1.7905	-0.352	4.2199	0.074	-0.354	-0.2157	0.2785	0.0917	0.0627	0.2783	-0.2046	-0.1525	0.2491	0.0597	0.0229	0.2682	0.0006	0.18	7.7324	24.7187	13.3055
13	1.2185	0.0614	0.1009	1.6909	-0.1044	0.9146	-0.0748	-0.2262	0.1336	0.178	0.0594	0.0581	-0.1511	-0.0506	0.0118	0.2268	0.0433	-0.0212	0.2338	-0.0346	0.1814	7.581	37.8467	11.5909
14	1.6325	-1.3322	0.7896	2.5005	-0.4581	2.4339	-0.1668	-0.2368	0.3361	0.2931	0.1089	-0.1727	-0.2495	0.04	0.0569	0.2438	0.0213	-0.0759	0.2403	-0.0701	0.2271	20.3096	39.705	16.1213
15	1.2385	-0.7382	0.8198	0.8992	-0.3751	1.2738	-0.0588	-0.1224	0.0929	0.09	0.0524	-0.1407	0.0463	0.0859	0.0141	0.1802	-0.0146	-0.012	0.2129	-0.0111	0.1956	19.6658	30.7819	2.1984
16	0.9145	-0.8134	0.017	1.1086	0.3011	1.149	0.01	0.1075	0.1526	-0.1184	0.0157	-0.2226	-0.1527	0.1773	-0.0185	0.1797	-0.058	0.0217	0.1939	0.0028	0.1981	18.7364	36.3976	-20.6659
17	2.1121	-0.8151	0.1567	0.6796	-0.7089	3.0804	-0.0433	0.1268	0.3206	-0.1915	0.0256	-0.2696	-0.2032	0.2922	0.0097	0.2249	-0.0736	0.0223	0.1815	-0.0153	0.2758	23.2318	45.6324	-18.5525
18	1.296	-0.6766	-0.3072	1.7982	0.0281	0.9939	-0.0187	-0.0642	0.3969	0.0114	0.0495	-0.3538	-0.2211	0.2102	-0.026	0.2474	-0.0703	-0.0128	0.205	-0.024	0.3095	18.0101	52.751	-10.6771
19	2.5284	0.6141	-0.8213	4.5492	-2.0704	2.9546	0.0503	0.0377	0.4886	0.1621	0.046	-0.2848	-0.5206	0.0479	-0.0699	0.2287	-0.0143	0.0155	0.1666	-0.0264	0.2617	12.765	53.3553	-10.1798
20	1.7258	0.7105	0.9999	0.385	0.5382	2.4876	0.0455	-0.0931	-0.2611	0.1909	0.0824	-0.1443	0.2968	0.2062	-0.1499	0.2405	0.0467	-0.0237	0.1736	-0.0127	0.1846	20.1322	20.8591	11.3803
21	2.8886	-0.1713	0.0809	2.3004	-0.0904	1.9844	0.0533	-0.2036	-0.2958	0.1283	-0.0038	0.018	0.2583	0.092	-0.0447	0.1965	-0.005	-0.0126	0.1747	0.0378	0.1803	11.0256	8.2784	-5.3418
22	4.5253	2.1257	-2.7532	2	2.0859	4.579	-0.3431	0.0003	-0.3761	-0.462	-0.1235	0.3292	-0.5952	0.2952	0.4649	0.3141	-0.0502	-0.0892	0.2212	0.0183	0.2576	9.4661	34.4592	0.7162
23	2.6551	0.4021	0.8869	1.9047	0.1039	3.4466	0.2175	0.0393	-0.4905	0.0151	-0.059	-0.1672	0.7299	-0.0427	-0.137	0.2978	0.0135	0.0054	0.2577	-0.063	0.3114	32.2294	2.2281	-34.4496
24	3.3783	-0.267	1.3361	0.3778	0.4854	1.434	0.2206	-0.4166	-0.3932	0.1798	0.023	-0.0315	0.2193	-0.0488	-0.2467	0.2652	-0.0458	0.0021	0.2636	0.0277	0.2652	21.7818	8.2115	-21.3514
25	0.6948	-0.01	0.1496	0.6654	0.4637	2.4956	0.0833	0.0473	-0.2437	0.0074	-0.0158	0.016	0.4015	-0.0366	-0.0597	0.1958	0.0096	-0.026	0.1381	-0.0029	0.2521	2.3342	4.4759	-24.3678
26	1.0425	-0.7538	-0.3338	2.572	1.4433	2.1584	-0.0256	-0.093	-0.0025	0.2744	0.1645	-0.5143	0.2388	0.2848	-0.1182	0.1649	-0.0178	-0.0255	0.3075	-0.0152	0.3175	35.0367	19.1831	-17.7214
27	5.7177	1.8496	0.7213	2.8151	2.8507	3.1977	0.0877	-1.7139	-0.8594	-0.2489	-0.3263	0.2518	-0.0037	2.5104	0.2556	0.1574	0.0275	-0.0315	0.444	-0.0999	0.33	22.0239	9.5045	-31.3692
28	0.949	-0.2693	0.554	0.555	-0.202	0.91	0.0997	0.2212	-0.0878	-0.2244	-0.0797	0.0497	0.0559	0.0715	-0.0209	0.2586	0.0446	-0.0321	0.2631	-0.0564	0.2041	-7.8866	17.6326	-55.9888
29	1.0465	-0.3518	0.0042	1.7085	0.2304	0.8823	0.064	0.2692	0.1032	-0.2966	-0.049	-0.2626	-0.1841	0.2348	-0.0211	0.2314	-0.0219	0.0456	0.2662	0.0225	0.1697	14.022	32.2622	-45.9377
30	0.2271	0.0825	0.2462	0.5242	0.2577	1.7608	0.0187	0.0953	-0.0122	-0.0928	-0.0644	0.1587	-0.1489	-0.2241	0.0366	0.1538	0.0336	-0.0365	0.2101	-0.0321	0.2128	-21.7232	26.7181	-42.5274
31	4.5445	2.4837	4.8812	6.7364	1.1979	5.645	-0.4849	0.0595	0.1525	-0.7829	0.4968	1.7192	-0.0216	0.8968	-0.0239	0.2473	0.0251	-0.0255	0.3092	-0.069	0.2604	-2.7777	19.1412	-47.8707

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 112 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 113 through 150 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 151 through 215 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 216 through 279 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 280 through 305 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 306 through 350 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 351 through 383 )
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 384 through 424 )
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 425 through 469 )
22	X-RAY DIFFRACTION	22	chain 'B' and (resid 503 through 503 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 10 through 165 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 166 through 215 )
25	X-RAY DIFFRACTION	25	chain 'C' and (resid 216 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 383 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 384 through 469 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 503 through 503 )

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