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

ID or keywords:

Entry

Database: PDB / ID: 8cfd

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment A07

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: 1.88 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 A07
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	8cfd.cif.gz	750.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8cfd.ent.gz	620.9 KB	Display	PDB format
PDBx/mmJSON format	8cfd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cfd_validation.pdf.gz	1.8 MB	Display	wwPDB validaton report
Full document	8cfd_full_validation.pdf.gz	1.8 MB	Display
Data in XML	8cfd_validation.xml.gz	79.4 KB	Display
Data in CIF	8cfd_validation.cif.gz	116.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfd ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfd	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)	178.760, 105.140, 108.250
Angle α, β, γ (deg.)	90.00, 99.71, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	C-799- 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) / 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) / 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, 1429 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-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#7: Chemical	ChemComp-R8A / (2-aminopyridin-3-yl)methanol Mass: 124.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₈N₂O / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1398 / 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: 2.42 Å³/Da / Density % sol: 49.23 %
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: 1.88→49.48 Å / Num. obs: 156983 / % possible obs: 98.4 % / Redundancy: 4.42 % / CC_1/2: 0.996 / R_merge(I) obs: 0.13 / R_rim(I) all: 0.147 / Net I/σ(I): 8.29

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
1.88-2	1.748	23535	0.457	1.977	1
2-2.13	0.985	24131	0.7	1.112	1
2.13-2.31	0.546	22448	0.86	0.621	1
2.31-2.52	0.323	20687	0.943	0.366	1
2.52-2.82	0.2	18742	0.979	0.225	1
2.82-3.26	0.118	16541	0.991	0.134	1
3.26-3.98	0.066	13934	0.995	0.075	1
3.98-5.62	0.045	10837	0.997	0.052	1
5.62-49.48	0.036	6128	0.999	0.041	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: 1.88→43.38 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.93 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2161	2097	1.34 %
R_work	0.1743	-	-
obs	0.1749	156820	98.36 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.88→43.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14218	0	316	1398	15932

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	14972
X-RAY DIFFRACTION	f_angle_d	0.722	20324
X-RAY DIFFRACTION	f_dihedral_angle_d	13.143	5566
X-RAY DIFFRACTION	f_chiral_restr	0.05	2267
X-RAY DIFFRACTION	f_plane_restr	0.005	2692

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 (%)
1.88-1.93	0.5407	113	0.5076	8293	X-RAY DIFFRACTION	80
1.93-1.97	0.4198	141	0.4076	10420	X-RAY DIFFRACTION	100
1.97-2.03	0.3214	141	0.3248	10419	X-RAY DIFFRACTION	100
2.03-2.09	0.2998	140	0.28	10423	X-RAY DIFFRACTION	100
2.09-2.16	0.2691	141	0.251	10450	X-RAY DIFFRACTION	100
2.16-2.23	0.252	142	0.235	10438	X-RAY DIFFRACTION	100
2.23-2.32	0.2505	142	0.2056	10423	X-RAY DIFFRACTION	100
2.32-2.43	0.2404	141	0.1782	10439	X-RAY DIFFRACTION	100
2.43-2.56	0.2172	142	0.1773	10473	X-RAY DIFFRACTION	100
2.56-2.72	0.2507	143	0.1781	10489	X-RAY DIFFRACTION	100
2.72-2.92	0.2251	141	0.1637	10447	X-RAY DIFFRACTION	100
2.92-3.22	0.1835	143	0.1635	10502	X-RAY DIFFRACTION	100
3.22-3.68	0.1977	141	0.1462	10445	X-RAY DIFFRACTION	99
3.69-4.64	0.168	142	0.1252	10444	X-RAY DIFFRACTION	99
4.64-43.38	0.1913	144	0.1474	10618	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	1.5068	-1.9091	0.0697	2.5422	-0.5074	3.7483	-0.094	0.1976	-0.3769	-0.1225	-0.059	0.467	0.1656	-0.531	0.1471	0.3367	-0.1055	0.0427	0.4335	-0.0756	0.5284	4.5859	-1.1264	19.6656
2	1.9401	-0.2843	-0.3457	1.4914	-0.4175	2.041	-0.0324	0.1583	-0.2703	0.0385	0.024	0.4043	0.1814	-0.408	0.0006	0.2941	-0.0816	0.0643	0.3944	-0.051	0.4946	2.5371	1.7573	31.4297
3	1.1379	0.3442	-0.7572	0.6742	-0.3181	1.8788	0.0276	-0.0874	-0.0009	0.1969	-0.0162	0.308	-0.0902	-0.251	-0.0158	0.3291	0.0058	0.0979	0.3089	-0.0328	0.4474	9.6412	10.682	40.4245
4	1.1394	0.0143	0.4733	0.5886	0.1367	1.4342	0.0117	0.0114	0.2398	0.0223	-0.0238	0.1523	-0.2234	-0.1621	0.0137	0.3117	0.025	0.0485	0.2594	-0.0009	0.4114	22.3598	28.4014	29.9624
5	1.1627	1.0476	-0.323	3.0266	-0.9687	3.3403	0.0113	0.1665	0.3011	0.0987	-0.0355	0.2093	-0.5459	-0.3585	-0.0115	0.3264	0.0548	0.0336	0.3329	0.0163	0.4764	14.0529	27.5696	19.6761
6	2.7116	0.1044	0.6739	2.1412	0.2661	0.2904	-0.0108	-0.494	-0.1627	0.5774	-0.0488	0.4631	0.2463	-0.2745	0.0715	0.3865	-0.0459	0.1359	0.343	0.0268	0.4427	8.4914	-0.1622	47.7142
7	1.5038	-0.324	0.3313	1.3289	-0.055	0.9938	-0.074	-0.202	-0.2499	0.2631	0.054	0.2061	0.2614	-0.0145	0.0163	0.4236	0.018	0.1063	0.2711	0.0331	0.356	30.7758	-5.3821	46.4461
8	2.0003	1.9996	1.9993	2.0002	2.0003	2.0009	0.6991	-0.7168	0.9829	0.3022	-1.9248	0.9848	0.4634	-0.7349	1.2507	0.417	-0.0246	0.0334	0.4262	0.0315	0.4591	14.0302	7.8333	29.8519
9	1.6481	-0.3857	-0.5655	2.0299	0.0807	1.1738	0.0858	0.3333	0.2027	-0.4228	-0.0849	0.1842	-0.1625	-0.2718	-0.0036	0.4245	0.0624	-0.0648	0.4232	0.0391	0.3274	21.9526	23.662	-3.6109
10	3.0115	0.9933	-0.7486	1.5592	-0.1056	2.3546	-0.0235	0.589	-0.1038	-0.4387	-0.0108	0.1363	0.1116	-0.5073	0.0387	0.6493	0.0548	-0.0832	0.5473	-0.028	0.2946	26.4219	13.2107	-15.5991
11	1.6012	0.1731	-1.1223	1.4833	-0.3274	2.2715	0.0393	0.3072	0.0859	-0.5226	-0.0698	-0.0784	-0.0518	0.0076	0.0386	0.393	0.0363	0.0229	0.2761	0.0198	0.264	37.2832	14.4309	-3.4867
12	1.6795	-0.1417	-0.2057	0.7596	0.0921	0.963	-0.0486	0.1514	-0.1718	-0.1593	-0.0253	0.1189	0.1704	-0.1143	0.0732	0.3472	-0.0131	0.018	0.2573	-0.0301	0.3064	32.8167	-2.9231	11.6667
13	1.0778	-0.5416	0.3377	1.5723	0.8418	0.9014	0.1421	0.3328	0.1852	-0.5798	-0.0229	-0.2623	-0.3061	0.1981	-0.1553	0.5335	0.0068	0.0666	0.3532	0.0645	0.3891	40.8751	25.246	-10.5757
14	1.7657	-0.239	0.0761	1.6625	0.6149	2.2738	-0.0115	0.2011	0.4155	-0.3183	0.0576	-0.0991	-0.4333	0.2462	-0.0395	0.4103	-0.0312	0.0596	0.2881	0.0729	0.4085	49.8029	32.7862	9.0108
15	7.4213	-0.7324	1.3672	2	-1.7765	2.0001	2.0414	1.0767	0.392	-0.8544	-1.7188	-0.4339	0.8845	0.3679	-0.3664	0.3448	-0.0157	-0.1724	0.4625	0.136	0.4916	28.8532	16.6727	3.4711
16	0.9396	1.7188	0.6035	3.549	0.3482	2.5395	-0.1321	-0.1842	-0.2652	0.1751	0.1224	-0.5079	0.1009	0.7118	0.0265	0.3244	0.1245	0.011	0.6231	-0.0219	0.4504	77.5205	7.4311	33.0683
17	1.1617	0.434	-0.3069	1.1889	0.1499	1.5041	-0.0231	-0.2055	-0.0631	0.0516	-0.0105	-0.1861	0.164	0.3852	0.01	0.292	0.0392	0.0251	0.5185	0.0054	0.4313	76.0816	9.7787	22.3043
18	1.9554	0.9828	0.1082	1.6033	0.9991	3.8771	-0.0203	-0.172	0.2869	0.0484	0.1126	-0.1344	-0.208	0.6124	-0.0835	0.3174	-0.0489	0.053	0.5985	-0.0343	0.498	82.7218	22.8855	18.6042
19	1.0552	-0.1905	-0.9527	0.1239	0.0988	1.8783	0.0346	0.0837	0.0945	-0.0583	0.0014	-0.1993	-0.1206	0.241	-0.0464	0.3009	-0.0274	0.0533	0.3688	0.0103	0.4153	67.4604	20.461	14.7243
20	0.9375	-0.1656	0.4032	0.8234	0.2346	2.2897	0.0162	-0.0568	0.2721	0.0224	-0.0113	-0.0921	-0.308	0.221	0.0018	0.3003	-0.0451	0.0457	0.2516	-0.0107	0.3911	52.4755	32.5448	27.9451
21	1.9904	-1.4665	-0.9931	3.3383	0.9171	3.5485	-0.0761	-0.2605	0.4546	0.2586	0.1009	-0.1632	-0.4001	0.4875	-0.0737	0.3386	-0.0735	-0.0116	0.4168	-0.0583	0.4573	60.9948	32.058	38.0983
22	1.6077	0.5661	0.0084	0.3367	-0.36	0.3302	-0.051	0.2682	-0.0342	-0.1475	0.0535	-0.1943	0.1294	0.2436	-0.0041	0.3617	0.0467	0.088	0.3663	-0.0168	0.3653	62.3065	6.4986	5.4256
23	3.7388	1.401	1.6439	2.9286	0.8969	3.5355	0.4822	1.3644	0.9505	0.2344	-1.8807	-0.9672	0.2047	0.8621	1.3974	0.3084	-0.0463	0.0761	0.4647	-0.0784	0.5962	65.868	15.2628	24.4684
24	1.1092	-0.127	-0.5072	1.0186	0.1826	1.5407	-0.1201	-0.3354	0.0081	0.5119	0.1216	-0.0807	0.2008	0.3524	0.0002	0.5023	0.0813	-0.0334	0.3735	-0.0242	0.2823	50.9373	15.1108	61.2798
25	1.7843	0.362	0.1211	0.8589	0.2846	1.0808	-0.0387	-0.0866	-0.1501	0.1834	0.0266	-0.0509	0.2448	0.1401	0.009	0.3817	0.0692	0.0357	0.2736	0.0249	0.2971	48.5422	-3.6574	39.4247
26	2.0031	-0.5403	-0.4688	3.5613	1.1579	2.3399	-0.0022	-0.0661	-0.2734	0.0946	0.057	-0.4601	0.4259	0.4517	-0.0699	0.3702	0.104	0.0093	0.3796	0.0255	0.3686	61.4146	-1.4548	41.7789
27	0.7501	-0.1143	0.2375	0.5495	-0.1306	1.2692	-0.0636	-0.2425	0.0254	0.3146	0.0779	0.1292	-0.0085	-0.0746	-0.0086	0.4081	0.028	0.0705	0.2568	-0.0394	0.2995	30.7393	21.703	57.2691
28	9.2473	6.1944	-5.2811	1.9999	5.7147	2.0001	2.9473	-0.5112	-0.6565	2.6704	-1.2314	-0.7608	1.2146	-1.5341	-1.7249	0.4711	0.0361	-0.141	0.6557	-0.0902	0.386	49.9035	14.8864	51.5921

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 8 through 34 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 35 through 134 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 135 through 215 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 216 through 350 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 351 through 383 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 384 through 424 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 425 through 469 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 502 through 502 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 9 through 112 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 113 through 150 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 151 through 215 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 216 through 383 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 384 through 424 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 425 through 469 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 502 through 502 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 8 through 34 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 35 through 112 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 113 through 149 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 150 through 215 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 216 through 350 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 351 through 383 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 384 through 469 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 502 through 502 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 9 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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