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

ID or keywords:

Entry

Database: PDB / ID: 8cfo

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment F04

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: 2.13 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 F04
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	8cfo.cif.gz	753.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8cfo.ent.gz	627.8 KB	Display	PDB format
PDBx/mmJSON format	8cfo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cfo_validation.pdf.gz	5.1 MB	Display	wwPDB validaton report
Full document	8cfo_full_validation.pdf.gz	5.2 MB	Display
Data in XML	8cfo_validation.xml.gz	80.6 KB	Display
Data in CIF	8cfo_validation.cif.gz	113.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfo ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfo	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

216 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)	177.760, 105.290, 107.710
Angle α, β, γ (deg.)	90.00, 99.72, 90.00
Int Tables number	5
Space group name H-M	C121

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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 , 7 types, 1105 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-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO₄
#6: Chemical	ChemComp-RB7 / N-[(4-bromo-3-methylphenyl)methyl]-2-(methylsulfonyl)ethan-1-amine Mass: 306.219 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₁₁H₁₆BrNO₂S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1062 / 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: 2.4 Å³/Da / Density % sol: 48.76 %
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: 2.13→47.6 Å / Num. obs: 109196 / % possible obs: 99.3 % / Redundancy: 4.48 % / CC_1/2: 0.994 / R_merge(I) obs: 0.162 / R_rim(I) all: 0.184 / Net I/σ(I): 7.96

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.13-2.25	1.487	17236	0.429	1.698	1
2.25-2.41	0.967	16556	0.66	1.095	1
2.41-2.6	0.667	15455	0.773	0.755	1
2.6-2.85	0.398	14245	0.923	0.447	1
2.85-3.18	0.23	12930	0.969	0.259	1
3.18-3.67	0.117	11409	0.99	0.133	1
3.67-4.49	0.062	9656	0.996	0.071	1
4.49-6.33	0.051	7496	0.997	0.058	1
6.33-47.6	0.037	4213	0.999	0.042	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: 2.13→34.92 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.68 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2188	2099	1.92 %
R_work	0.171	-	-
obs	0.1719	109122	99.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.13→34.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14218	0	527	1062	15807

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	15179
X-RAY DIFFRACTION	f_angle_d	0.965	20609
X-RAY DIFFRACTION	f_dihedral_angle_d	15.8	5671
X-RAY DIFFRACTION	f_chiral_restr	0.056	2266
X-RAY DIFFRACTION	f_plane_restr	0.007	2703

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 (%)
2.13-2.18	0.3713	130	0.3702	6620	X-RAY DIFFRACTION	93
2.18-2.23	0.3651	140	0.3329	7170	X-RAY DIFFRACTION	100
2.23-2.29	0.3821	141	0.3056	7175	X-RAY DIFFRACTION	100
2.29-2.36	0.3076	140	0.263	7129	X-RAY DIFFRACTION	100
2.36-2.43	0.3008	140	0.2478	7123	X-RAY DIFFRACTION	100
2.43-2.52	0.2991	140	0.2346	7129	X-RAY DIFFRACTION	99
2.52-2.62	0.2401	140	0.2042	7168	X-RAY DIFFRACTION	100
2.62-2.74	0.2609	141	0.1932	7169	X-RAY DIFFRACTION	100
2.74-2.88	0.2696	140	0.172	7146	X-RAY DIFFRACTION	100
2.88-3.07	0.2138	141	0.1695	7207	X-RAY DIFFRACTION	100
3.07-3.3	0.193	141	0.1528	7151	X-RAY DIFFRACTION	100
3.3-3.63	0.2001	141	0.1406	7208	X-RAY DIFFRACTION	100
3.63-4.16	0.1683	141	0.1285	7167	X-RAY DIFFRACTION	100
4.16-5.24	0.1906	140	0.1227	7182	X-RAY DIFFRACTION	99
5.24-34.92	0.1677	143	0.1573	7279	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	1.4454	-0.236	-0.6461	1.7754	-0.2541	2.1383	-0.0917	0.1993	-0.2413	-0.0197	-0.0466	0.4747	0.3232	-0.4904	0.1119	0.3228	-0.1043	0.025	0.4702	-0.104	0.5354	5.1656	-0.622	27.5387
2	1.7341	-0.1862	0.7359	1.0233	-0.5394	2.8475	-0.029	-0.0785	0.0469	0.0192	-0.0613	0.3136	-0.1493	-0.7079	0.0795	0.3642	0.0136	0.0955	0.622	-0.0961	0.5932	-1.2343	10.0898	40.6655
3	0.8577	-0.09	0.0883	0.8037	0.1937	1.4141	-0.0489	0.0152	0.0862	-0.0368	-0.033	0.2249	-0.2684	-0.2781	0.0762	0.3424	0.0567	-0.0198	0.3283	-0.0408	0.3802	20.0451	24.9076	28.9109
4	1.6488	-0.3893	-0.0472	0.4689	0.2712	0.9362	-0.169	-0.3412	-0.3277	0.2711	0.0401	0.2335	0.3571	-0.2247	0.1233	0.4975	-0.0269	0.1284	0.3938	0.0465	0.4671	19.8133	-2.7682	46.6964
5	2	2	2	2	8.8727	2	1.1002	-1.4703	1.3826	0.8129	-3.5553	2.2365	1.0521	-1.7893	2.4645	0.4406	-0.0721	0.0704	0.434	0.0224	0.4936	13.7573	7.8827	29.5935
6	1.3623	-0.5777	-0.1923	1.1098	-0.0623	1.9763	0.0832	0.3083	0.1173	-0.7172	-0.1804	0.2754	-0.3689	-0.459	0.0738	0.6596	0.1478	-0.1478	0.5001	-0.0278	0.3599	21.4598	23.4517	-3.8921
7	3.3054	0.7726	0.1143	1.3108	0.0453	3.2682	0.0447	0.7236	-0.1363	-0.7594	-0.2312	0.0756	0.2205	-0.465	0.1901	0.8732	0.0611	-0.0508	0.5949	-0.0606	0.3289	31.0608	13.2848	-15.2069
8	1.1521	0.0468	-0.3271	1.1106	0.0211	0.9029	-0.0684	0.1864	-0.1811	-0.2211	-0.0336	0.119	0.1599	-0.1414	0.1033	0.4061	-0.0106	-0.0077	0.3033	-0.0599	0.3117	33.0597	0.3835	10.1713
9	1.8455	-0.79	0.6821	2.3521	1.1968	1.7789	0.1765	0.6352	0.3352	-0.9957	-0.0243	-0.4725	-0.7254	0.0404	-0.1687	0.7695	-0.0075	0.0467	0.4263	0.0606	0.413	40.2237	25.0428	-10.8666
10	2.7461	-0.1484	0.0516	1.0237	-0.0114	2.4249	-0.1561	0.2394	0.4164	-0.3604	0.0408	0.0325	-0.3902	0.3137	0.1225	0.5217	-0.0521	0.0207	0.2997	0.0651	0.3896	49.3184	32.7222	8.6192
11	2	-5.9946	9.9448	3.6314	-0.028	9.1323	0.9604	0.3464	0.792	-0.2456	-2.0488	-1.9591	2.146	0.0255	1.0843	0.7564	-0.0053	-0.0297	0.2341	0.039	0.3738	28.4615	16.5382	3.1773
12	0.6436	1.4852	-0.0891	3.4679	0.0319	3.1359	-0.1752	-0.4116	-0.145	0.1776	-0.0868	-0.3622	-0.0368	0.4913	0.2508	0.3906	0.141	-0.0189	0.5882	0.0627	0.4554	77.0711	7.665	32.7597
13	2.3769	-0.0313	-1.7927	1.1309	-0.1255	2.1737	-0.0787	-0.1283	-0.2721	-0.1115	-0.1179	-0.2576	0.3139	0.4131	0.1874	0.3933	0.1341	0.0898	0.4991	0.1063	0.4511	74.1419	4.502	16.0194
14	0.3343	0.1962	0.0089	1.2843	0.0127	1.3	0.0519	-0.0908	0.0263	-0.0263	-0.0661	-0.278	0.0299	0.3693	0.0081	0.3577	0.0111	0.0091	0.6242	0.0323	0.5381	76.6229	13.5552	25.9895
15	1.4216	0.7321	-0.5104	2.6036	1.5605	4.5371	-0.1575	-0.2602	0.2311	0.1601	0.1296	-0.2592	-0.2014	0.9415	0.0275	0.3115	-0.0639	-0.0003	0.7084	0.0894	0.571	82.3291	23.2577	18.3464
16	1.5849	0.1727	-1.0374	0.265	0.1011	2.248	0.0002	0.1178	0.064	-0.0406	0.0092	-0.283	-0.2157	0.236	-0.0065	0.3082	-0.0066	0.0328	0.3421	0.0526	0.414	66.68	20.4007	14.3978
17	1.3938	-0.5999	0.4823	0.4088	0.3645	2.5145	0.0196	-0.0028	0.125	-0.0598	-0.1059	-0.0734	-0.2959	0.0943	0.0496	0.3157	-0.0353	-0.0169	0.2118	0.0143	0.2963	46.1155	28.279	23.0786
18	1.0842	-0.4017	0.0675	0.8891	-0.129	2.4963	-0.0412	-0.0917	0.3624	0.066	-0.0523	-0.2228	-0.5065	0.3039	0.1126	0.5063	-0.1062	-0.0457	0.324	-0.0009	0.426	57.1494	36.2263	31.3998
19	3.1207	-2.136	-1.5935	5.1831	1.5611	5.2338	-0.1678	-0.2143	0.5633	0.3974	0.1228	-0.3034	-0.4895	0.5444	0.0159	0.4106	-0.0569	-0.102	0.4234	-0.0043	0.4055	60.5068	32.076	37.6664
20	4.0693	0.0872	0.1597	1.9638	-0.0187	0.0029	-0.0967	0.7264	0.0356	-0.4358	-0.098	-0.335	0.3111	0.3979	0.1842	0.3337	0.0545	0.0814	0.5328	0.0551	0.458	72.4351	12.2485	5.3974
21	2.4658	0.3424	0.6057	0.9195	-0.3158	1.7228	0.0004	0.3839	-0.153	-0.4185	0.0595	-0.2034	0.096	0.1851	-0.0671	0.4884	0.0376	0.0915	0.3147	-0.0068	0.3416	52.422	1.5649	4.9097
22	4.5033	2.5176	-0.1918	2.5264	1.5415	2.4377	1.6359	2.0439	2.9397	-1.8347	-3.1196	-2.9349	1.3922	2.0143	1.4838	0.3582	0.1392	0.1182	0.5728	-0.0516	0.6223	65.4631	15.4323	24.0833
23	1.1616	-0.4348	-0.5648	1.0581	0.0582	2.026	-0.2102	-0.4435	0.0152	0.6991	0.1169	-0.166	0.1032	0.4791	0.1099	0.6494	0.0859	-0.1048	0.5274	-0.0241	0.3369	54.4126	18.1928	62.2583
24	1.7161	0.0759	-0.4465	0.7608	-0.0876	2.8039	-0.259	-0.4037	-0.1709	0.6123	0.0922	0.0369	0.2314	-0.036	0.1774	0.6034	0.1096	0.0368	0.363	0.0554	0.3444	42.4922	9.0296	57.5026
25	1.891	0.1418	0.1394	0.9903	0.3767	1.1013	-0.1098	-0.0995	-0.3001	0.1804	0.0408	-0.0619	0.3138	0.1554	0.066	0.4398	0.0746	0.0346	0.3117	0.048	0.3238	48.2502	-3.5188	39.0304
26	2.1731	0.0152	-1.0452	3.5111	1.6893	2.8593	-0.0522	-0.2003	-0.2844	0.0708	0.1195	-0.5602	0.4233	0.5612	-0.0451	0.414	0.1349	-0.0009	0.4306	0.0592	0.3975	61.0699	-1.2534	41.3353
27	0.8025	-0.2192	0.2577	0.6709	0.0765	1.6416	-0.1414	-0.3429	0.0054	0.4801	0.1165	0.1888	-0.0641	-0.1334	0.0336	0.5539	0.1009	0.0549	0.3962	-0.024	0.3475	30.4767	21.6644	56.8446
28	5.0348	-0.6236	-2.9655	0.9371	-0.227	2.1575	2.6266	-0.6802	0.1684	2.9384	-1.6974	-0.1731	1.3373	-0.7203	-0.9476	0.5767	0.073	-0.0844	0.5146	-0.0829	0.2274	49.6571	14.8942	51.1542

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 112 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 113 through 178 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 179 through 383 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 384 through 469 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 502 through 502 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 9 through 112 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 113 through 178 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 179 through 383 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 384 through 424 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 425 through 469 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 502 through 502 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 8 through 34 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 35 through 63 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 64 through 112 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 113 through 150 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 151 through 215 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 216 through 279 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 280 through 350 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 351 through 383 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 384 through 424 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 425 through 469 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 502 through 502 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 9 through 150 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 151 through 215 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 216 through 350 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 351 through 383 )
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 384 through 469 )
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 502 through 502 )

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Protein , 1 types, 4 molecules ABCD

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