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

ID or keywords:

Entry

Database: PDB / ID: 8cfl

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment E07

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: 1.73 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 E07
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	8cfl.cif.gz	752.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8cfl.ent.gz	621.8 KB	Display	PDB format
PDBx/mmJSON format	8cfl.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cfl_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	8cfl_full_validation.pdf.gz	2 MB	Display
Data in XML	8cfl_validation.xml.gz	79.9 KB	Display
Data in CIF	8cfl_validation.cif.gz	118.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfl ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfl	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

212 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)	178.450, 104.830, 107.590
Angle α, β, γ (deg.)	90.00, 99.44, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-754- HOH

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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, 1539 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-R9Y / 1-(1-methyl-1,2,3,4-tetrahydroquinolin-6-yl)methanamine Mass: 176.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₆N₂ / Feature type: SUBJECT OF INVESTIGATION
#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.: 15 / Source method: obtained synthetically / Formula: PO₄
#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.: 1508 / 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: 48.72 %
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→47.5 Å / Num. obs: 203188 / % possible obs: 99.3 % / Redundancy: 4.55 % / CC_1/2: 0.997 / R_merge(I) obs: 0.124 / R_rim(I) all: 0.141 / Net I/σ(I): 9.09

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.73-1.83	2.168	31977	0.435	2.448	1
1.83-1.96	1.296	30979	0.675	1.462	1
1.96-2.11	0.708	28825	0.854	0.8	1
2.11-2.32	0.384	26474	0.941	0.438	1
2.32-2.59	0.224	24070	0.974	0.255	1
2.59-2.99	0.127	21195	0.991	0.143	1
2.99-3.65	0.067	17929	0.996	0.077	1
3.65-5.15	0.037	13930	0.998	0.043	1
5.15-47.5	0.03	7809	0.999	0.034	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→29.32 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.74 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2014	2131	1.05 %
R_work	0.1653	-	-
obs	0.1657	202864	99.21 %

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→29.32 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14204	0	329	1508	16041

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	14960
X-RAY DIFFRACTION	f_angle_d	0.95	20307
X-RAY DIFFRACTION	f_dihedral_angle_d	13.382	5575
X-RAY DIFFRACTION	f_chiral_restr	0.06	2263
X-RAY DIFFRACTION	f_plane_restr	0.007	2686

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	0.4311	132	0.4516	12439	X-RAY DIFFRACTION	93
1.77-1.81	0.4861	143	0.4015	13458	X-RAY DIFFRACTION	100
1.81-1.86	0.3727	142	0.3465	13379	X-RAY DIFFRACTION	100
1.86-1.91	0.3374	142	0.301	13389	X-RAY DIFFRACTION	100
1.91-1.98	0.2879	142	0.2737	13386	X-RAY DIFFRACTION	99
1.98-2.05	0.2906	142	0.2532	13371	X-RAY DIFFRACTION	100
2.05-2.13	0.2703	143	0.2114	13412	X-RAY DIFFRACTION	100
2.13-2.23	0.2478	142	0.1896	13429	X-RAY DIFFRACTION	100
2.23-2.34	0.227	143	0.1768	13462	X-RAY DIFFRACTION	100
2.34-2.49	0.2201	143	0.1615	13412	X-RAY DIFFRACTION	100
2.49-2.68	0.1957	143	0.1574	13486	X-RAY DIFFRACTION	100
2.68-2.95	0.1828	143	0.1428	13493	X-RAY DIFFRACTION	100
2.95-3.38	0.1651	143	0.1375	13499	X-RAY DIFFRACTION	100
3.38-4.25	0.1577	143	0.1173	13435	X-RAY DIFFRACTION	99
4.25-29.32	0.1428	145	0.1318	13683	X-RAY DIFFRACTION	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	1.5793	-0.9702	0.0175	1.9372	-0.1	2.1936	-0.0431	0.125	-0.2967	-0.1542	-0.0642	0.4085	0.2277	-0.5367	0.1006	0.2894	-0.1138	0.0296	0.435	-0.0712	0.4077	5.0897	-0.8187	19.5062
2	1.0819	0.1019	-0.5301	0.5487	-0.2591	1.4437	-0.0355	0.0226	-0.0581	0.1052	0.0226	0.2569	0.0772	-0.3866	0.012	0.2391	-0.0301	0.0714	0.3113	-0.0299	0.3803	5.9593	5.805	35.3536
3	1.2104	0.0267	0.2987	0.5606	0.2384	1.5752	-0.0143	0.0356	0.2416	-0.0289	-0.0198	0.128	-0.2643	-0.1736	0.0422	0.249	0.0312	0.0308	0.2068	0.0051	0.3383	20.8901	28.1417	27.9399
4	1.8162	-0.1538	0.2527	0.5999	0.051	0.6315	-0.0719	-0.3286	-0.2186	0.2119	0.0247	0.2241	0.2225	-0.1372	0.0524	0.3243	-0.0175	0.1071	0.234	0.0238	0.3074	20.2692	-2.9419	46.7716
5	2.0046	1.9968	2.0097	2.0055	2.0022	2.0148	0.4322	-1.1626	0.3256	-0.5327	-2.2117	1.0433	0.0158	-1.1579	1.8089	0.2411	0.0544	0.0037	0.3964	-0.069	0.4431	14.1891	7.8346	29.7194
6	1.2528	-0.3723	-0.6003	1.9019	-0.0642	1.2691	0.0828	0.3451	0.2058	-0.3591	-0.0807	0.1838	-0.157	-0.2951	-0.0039	0.3053	0.0488	-0.0614	0.3729	0.0616	0.2748	21.9683	23.7105	-3.5534
7	2.9582	1.1166	-0.5321	2.0812	0.1455	2.3816	-0.1025	0.5215	-0.0573	-0.4076	-0.0332	0.1475	0.0513	-0.4528	0.1146	0.4509	0.0187	-0.0621	0.4939	-0.0041	0.2345	26.368	13.3252	-15.5219
8	1.5601	0.1021	-1.2423	1.0906	-0.2358	2.556	0.013	0.2904	0.0444	-0.3457	-0.0645	-0.0393	-0.0125	-0.0206	0.0417	0.3116	0.0191	0.0083	0.2546	0.025	0.2302	37.2265	14.4794	-3.4452
9	1.6388	-0.0794	-0.3513	0.7754	0.0915	1.0316	-0.0596	0.1315	-0.1637	-0.0864	-0.0129	0.1232	0.2198	-0.1096	0.072	0.2876	-0.0213	0.0179	0.2148	-0.022	0.2511	32.821	-2.8236	11.5493
10	0.7416	-0.2011	0.3816	0.4208	0.28	1.761	-0.0453	0.2107	0.1503	-0.2804	0.031	-0.1105	-0.3394	0.2312	0.0227	0.4222	-0.0353	0.0574	0.2748	0.0714	0.3549	45.4443	29.1306	-0.3675
11	6.4538	-1.9524	0.576	5.6499	0.826	9.6985	1.5493	1.4414	0.9683	-1.392	-1.6019	-0.7102	0.6481	-0.162	0.0269	0.2958	0.0264	-0.0611	0.2842	0.097	0.3183	28.8994	16.7028	3.5164
12	1.0438	-0.2086	-0.8237	1.3628	0.0216	1.0739	-0.0483	-0.2035	-0.0316	0.0429	0.0376	-0.2454	0.0838	0.4925	0.0019	0.2336	0.0434	0.0101	0.5588	0.005	0.3505	76.1654	9.1516	24.8625
13	2.9827	0.9807	0.0785	0.7945	0.2326	1.563	0.1101	-0.2383	0.268	0.0818	0.046	-0.1995	-0.1517	0.66	-0.1485	0.2392	-0.0685	0.0371	0.6594	-0.042	0.4346	82.5128	22.7482	18.4154
14	0.8787	-0.1478	-0.6805	0.2364	0.0015	1.7698	0.0668	0.0624	0.1715	-0.082	0.0248	-0.1522	-0.152	0.2942	-0.09	0.213	-0.0328	0.0518	0.3266	0.0034	0.3082	67.3672	20.4216	14.6355
15	0.8445	-0.0891	0.4065	0.8036	0.0929	2.0998	0.0109	-0.0633	0.262	0.0079	-0.0017	-0.0851	-0.3334	0.262	0.0081	0.2471	-0.0534	0.0396	0.2168	-0.0132	0.3103	52.4945	32.3954	27.8611
16	1.5746	-1.4257	-0.7703	2.7353	0.738	2.8748	-0.0231	-0.2667	0.3512	0.1228	0.0075	-0.1299	-0.4283	0.2956	-0.0544	0.2708	-0.0822	-0.0022	0.3945	-0.0752	0.3663	61.0155	31.8771	37.9875
17	1.9648	0.6703	0.2065	0.5888	-0.3278	0.4603	-0.0866	0.3318	-0.043	-0.1765	0.0644	-0.1734	0.1104	0.2683	0.0308	0.2982	0.0395	0.0799	0.3496	-0.009	0.2972	62.2027	6.5557	5.3093
18	6.8961	0.0653	0.6654	4.5693	-1.4383	6.3717	0.2527	1.1093	1.3711	0.1335	-1.3009	-0.9691	0.3455	0.3011	1.0637	0.2762	-0.0374	0.0402	0.4491	-0.0665	0.4508	65.7701	15.2341	24.288
19	0.6274	-0.1085	-0.6319	1.7201	0.0347	1.5831	-0.0107	-0.2858	0.1121	0.3423	0.0447	-0.22	-0.0356	0.5348	-0.0345	0.3228	-0.004	-0.0594	0.4578	-0.075	0.2653	55.1865	21.6117	59.8473
20	3.1402	-1.2793	-0.1863	1.7572	-0.3639	2.5522	-0.1249	-0.3819	-0.1302	0.3974	0.1296	-0.1113	0.4942	0.8207	-0.0335	0.5552	0.155	-0.0476	0.5453	0.0073	0.2779	54.0054	8.2616	69.3283
21	1.3962	-0.0239	-1.0321	0.8722	0.2563	2.5155	-0.0995	-0.2571	-0.0502	0.343	0.0659	0.0237	0.2646	0.1351	0.0434	0.367	0.0444	0.0103	0.2404	0.002	0.2284	42.8539	8.8625	57.7169
22	1.4241	0.4266	-0.0071	0.9053	0.2698	1.0503	-0.0407	-0.1474	-0.1867	0.1314	0.0204	-0.1268	0.2763	0.2424	0.0165	0.3062	0.0832	0.0231	0.2649	0.0311	0.2475	51.0725	-3.2572	39.6448
23	0.4832	0.0371	0.2115	0.4556	-0.0036	1.3489	-0.0203	-0.2198	0.0365	0.2067	0.0369	0.1172	-0.0439	-0.0923	-0.0111	0.3331	0.0192	0.064	0.2663	-0.0448	0.2796	30.916	21.5412	57.0565
24	4.1375	4.2536	1.5889	4.3932	1.9714	6.2412	1.9254	1.1473	0.3804	1.1907	-0.0409	-0.6567	0.6133	0.2784	-1.8954	0.3674	0.0668	-0.0029	0.5081	-0.0656	0.355	50.0086	14.6532	51.3185

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 215 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 216 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 150 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 151 through 215 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 216 through 383 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 384 through 469 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 502 through 502 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 10 through 112 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 113 through 149 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 150 through 215 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 216 through 350 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 351 through 383 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 384 through 469 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 502 through 502 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 9 through 112 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 113 through 150 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 151 through 215 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 216 through 383 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 384 through 469 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 502 through 502 )

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Non-polymers , 7 types, 1539 molecules

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 7 types, 1539 molecules

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