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

ID or keywords:

Entry

Database: PDB / ID: 8cfi

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment D07

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: 2.02 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 D07
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	8cfi.cif.gz	747.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8cfi.ent.gz	621.1 KB	Display	PDB format
PDBx/mmJSON format	8cfi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cfi_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	8cfi_full_validation.pdf.gz	2 MB	Display
Data in XML	8cfi_validation.xml.gz	76.5 KB	Display
Data in CIF	8cfi_validation.cif.gz	109.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfi ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfi	HTTPS FTP

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Related structure data

Related structure data	6f3pS S: Starting model for refinement
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)	176.420, 104.110, 107.880
Angle α, β, γ (deg.)	90.00, 100.21, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-877- 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, 1169 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-SYJ / 2-fluoranyl-~{N}-(furan-2-ylmethyl)benzenesulfonamide Mass: 255.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₁H₁₀FNO₃S / 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.: 1139 / 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: 2.36 Å³/Da / Density % sol: 47.79 %
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: 2.02→46.74 Å / Num. obs: 125371 / % possible obs: 99.4 % / Redundancy: 4.52 % / CC_1/2: 0.996 / R_merge(I) obs: 0.128 / R_rim(I) all: 0.145 / Net I/σ(I): 9.05

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.02-2.14	1.383	19951	0.392	1.565	1
2.14-2.29	0.868	19016	0.569	0.991	1
2.29-2.47	0.576	17670	0.762	0.655	1
2.47-2.71	0.369	16375	0.898	0.416	1
2.71-3.02	0.21	14798	0.967	0.235	1
3.02-3.49	0.114	13101	0.991	0.129	1
3.49-4.27	0.057	11070	0.997	0.065	1
4.27-6.01	0.04	8566	0.998	0.045	1
6.01-46.74	0.029	4824	0.999	0.033	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
Starting model: 6F3P

6f3p

Resolution: 2.02→39.88 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.4 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2336	2098	1.67 %
R_work	0.192	-	-
obs	0.1927	125341	99.45 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.02→39.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14218	0	320	1139	15677

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14946
X-RAY DIFFRACTION	f_angle_d	0.496	20286
X-RAY DIFFRACTION	f_dihedral_angle_d	12.602	5551
X-RAY DIFFRACTION	f_chiral_restr	0.042	2262
X-RAY DIFFRACTION	f_plane_restr	0.003	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 (%)
2.02-2.06	0.3734	135	0.3741	7935	X-RAY DIFFRACTION	97
2.06-2.12	0.3672	139	0.3377	8198	X-RAY DIFFRACTION	100
2.12-2.17	0.361	140	0.314	8206	X-RAY DIFFRACTION	100
2.17-2.24	0.3553	140	0.3071	8198	X-RAY DIFFRACTION	100
2.24-2.31	0.3297	139	0.2771	8221	X-RAY DIFFRACTION	100
2.31-2.39	0.3006	140	0.2534	8226	X-RAY DIFFRACTION	100
2.39-2.49	0.2667	139	0.2458	8175	X-RAY DIFFRACTION	99
2.49-2.6	0.2769	140	0.2258	8216	X-RAY DIFFRACTION	100
2.6-2.74	0.2627	141	0.216	8260	X-RAY DIFFRACTION	100
2.74-2.91	0.2291	140	0.1966	8237	X-RAY DIFFRACTION	100
2.91-3.13	0.2276	141	0.1901	8249	X-RAY DIFFRACTION	100
3.13-3.45	0.2377	141	0.1745	8280	X-RAY DIFFRACTION	100
3.45-3.95	0.2191	141	0.152	8262	X-RAY DIFFRACTION	100
3.95-4.97	0.1643	141	0.1379	8267	X-RAY DIFFRACTION	100
4.97-39.88	0.195	141	0.1633	8313	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	1.5815	-1.624	-0.0376	2.0043	-0.2337	2.3735	-0.0227	0.2576	-0.1415	-0.2768	-0.142	0.41	0.2156	-0.4692	0.1334	0.3434	-0.1355	-0.026	0.4089	-0.1089	0.4695	4.0147	-1.279	19.5448
2	1.2527	-0.8039	-0.1774	1.8159	0.1005	1.057	-0.0636	0.0614	-0.2961	-0.061	0.0911	0.416	0.2286	-0.2495	-0.0334	0.3057	-0.0831	-0.0178	0.3763	-0.039	0.4562	5.0861	-0.456	30.5422
3	2.1408	-0.6086	0.6949	1.4714	-0.3772	3.9297	-0.032	-0.0118	0.0817	-0.0849	0.031	0.2765	-0.0903	-0.5155	-0.0094	0.2332	0.0118	-0.0103	0.4127	-0.0137	0.4999	-4.6504	9.7016	36.462
4	1.1665	-0.1479	-0.4486	0.6191	-0.2806	1.5707	-0.0614	-0.1781	-0.0156	0.0749	0.0418	0.0633	-0.0335	-0.0548	0.0241	0.2815	-0.0266	-0.0312	0.2949	-0.0341	0.384	11.2398	10.5874	39.8907
5	1.3117	-0.09	0.2582	1.3463	0.1086	1.3205	-0.0372	-0.0049	0.3973	-0.0339	-0.0125	-0.1191	-0.2442	-0.1001	0.0516	0.2628	0.0176	-0.0178	0.2353	0.0065	0.3843	21.7391	28.1724	29.496
6	1.6317	0.779	-0.7793	2.5493	0.9494	2.5884	0.0659	0.3597	0.4424	-0.3059	-0.0433	0.1716	-0.3103	-0.3952	-0.0232	0.2683	0.0411	-0.0523	0.3643	0.0551	0.4557	13.4554	27.2154	19.2395
7	2.05	-0.4847	-0.0423	0.9823	-0.0297	0.2986	-0.1264	-0.3406	-0.2319	0.2066	0.1217	0.1683	0.2131	-0.1226	0.0062	0.354	-0.0143	0.0216	0.3245	0.0394	0.3617	19.4367	-2.6619	46.8838
8	4.7473	5.0102	0.0173	2.0001	5.1963	4.9181	1.0066	-1.4474	0.7633	0.9815	-2.8702	1.6405	0.6878	-1.4787	1.8565	0.2881	-0.0768	0.0087	0.3276	-0.0508	0.5041	13.439	7.7289	29.6153
9	1.5433	-0.6314	-0.6012	0.7704	-0.4542	1.0683	0.3141	0.8935	0.1116	-1.0995	-0.3861	-0.0414	0.1066	-0.2793	0.0254	0.9144	0.1967	0.0115	0.7196	0.0561	0.3374	22.6548	20.1143	-7.289
10	1.5448	-0.136	-0.5757	0.6137	0.0334	1.5369	0.2174	0.5493	0.1608	-0.9772	-0.3709	-0.2671	-0.095	0.252	0.1392	0.9099	0.1857	0.2162	0.5676	0.1486	0.4028	36.6164	13.9394	-3.7532
11	2.355	-0.3473	-0.3226	0.8039	0.1435	0.7669	0.0182	0.3824	-0.2836	-0.2686	-0.129	0.0013	0.2127	-0.0804	0.107	0.4919	-0.0151	0.0566	0.3537	-0.0568	0.3455	32.1066	-3.1492	11.6247
12	0.0071	0.0187	-0.0431	0.2635	-0.5168	1.0377	0.3498	0.6444	0.1973	-1.1495	-0.2152	-0.7339	-0.194	-0.0427	-0.1636	1.0844	0.1375	0.4454	0.7896	0.2419	0.6975	40.3342	24.7028	-10.5896
13	1.9876	-0.47	-0.1489	0.7527	0.5623	1.9244	-0.0026	0.3814	0.6355	-0.3412	-0.0489	-0.3522	-0.3823	0.4273	0.0466	0.5351	-0.0375	0.1305	0.4773	0.2338	0.7417	49.1365	32.2577	8.6727
14	4.3364	0.1054	-4.386	3.5905	-0.875	5.5221	1.4523	2.1533	1.4592	-1.6119	-2.9072	-1.7379	2.1398	0.0291	1.3785	0.578	0.0942	0.1716	0.3806	0.025	0.6104	28.2626	16.0983	3.3126
15	1.4161	0.3189	-0.3966	1.6335	0.2262	2.0943	-0.0033	-0.0963	0.0886	-0.0246	-0.0196	-0.3458	0.0462	0.6065	0.0126	0.3426	0.0732	0.0804	0.572	0.0722	0.6396	77.5163	11.7159	24.4537
16	4.463	1.486	-0.0843	2.969	-0.0853	2.831	0.013	0.4572	0.6038	-0.0104	0.0991	0.1871	-0.2456	0.2712	-0.1029	0.3505	-0.0086	0.0949	0.5972	0.1631	0.7251	78.7448	21.9845	11.4978
17	1.5783	-0.1302	-1.2175	0.3625	0.34	2.6591	-0.0373	0.1948	0.1904	-0.0905	-0.0498	-0.3671	-0.0637	0.1546	0.0685	0.4	0.0394	0.0809	0.4021	0.1038	0.6931	61.8839	19.987	16.371
18	0.8264	-0.3787	0.5654	0.7785	0.1133	1.8093	-0.0719	0.0257	0.4954	-0.0237	-0.0332	-0.4552	-0.2311	0.2186	0.1059	0.3692	-0.033	0.0167	0.3354	0.0716	0.7691	51.7211	32.2745	27.5866
19	2.203	-1.2749	-1.6556	1.7571	0.2224	3.063	-0.0631	-0.2286	0.5096	0.1235	0.2198	-0.522	-0.419	0.4515	-0.2346	0.3849	-0.0598	-0.0226	0.4185	-0.0068	0.7309	60.1852	31.9176	37.8673
20	2.1865	0.4483	-0.482	0.1921	-0.6095	0.9242	0.03	0.6044	0.0392	-0.2151	-0.0856	-0.4204	0.1586	0.3695	0.0645	0.5181	0.0946	0.2162	0.5178	0.0714	0.608	61.5232	6.208	5.4547
21	8.8827	1.653	1.7635	8.2628	1.3927	3.911	1.6932	2.5846	2.3762	-1.0485	-3.5189	-2.9702	0.6002	2.3899	1.8391	0.3944	0.1392	-0.0539	0.3922	0.0644	0.9351	64.9842	15.0423	24.3394
22	1.3265	-0.0279	-0.2529	0.9421	-0.0648	1.2294	-0.1254	-0.5107	0.1576	0.345	0.0528	-0.2666	-0.0042	0.2893	0.0751	0.4283	0.0772	-0.1022	0.4659	-0.0725	0.4468	50.1041	15.2696	61.0005
23	2.4885	0.1797	0.3442	1.1315	0.25	0.991	-0.063	-0.1081	-0.0839	0.1141	0.0401	-0.2268	0.217	0.1521	0.0249	0.3129	0.0496	-0.02	0.221	0.0135	0.3093	47.7979	-3.5443	39.3192
24	3.3841	-0.836	-1.0427	4.2878	1.7317	3.1111	0.0141	-0.2219	-0.0399	0.1606	0.1867	-1.0484	0.2846	0.572	-0.1641	0.3247	0.0728	-0.054	0.3619	-0.0024	0.586	60.5906	-1.3442	41.7384
25	2.5623	-0.8294	0.483	0.6645	-0.4045	1.5607	-0.1864	-0.5541	0.2639	0.3038	0.1514	-0.0086	-0.1115	-0.053	0.0329	0.456	0.0698	-0.0735	0.4166	-0.121	0.477	30.0354	21.7501	56.8361
26	8.2156	3.5515	-2.3011	2.0001	6.3769	6.52	1.1341	0.4319	0.2019	0.3056	-1.7141	0.0224	1.0114	-0.0137	0.5361	0.6135	0.1856	-0.2272	0.449	-0.1802	0.725	49.1929	14.886	51.1826

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 112 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 113 through 150 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 151 through 215 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 216 through 350 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 351 through 383 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 384 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 150 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 151 through 215 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 216 through 383 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 384 through 424 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 425 through 469 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 502 through 502 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 8 through 134 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 135 through 165 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 166 through 215 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 216 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 469 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 502 through 502 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 9 through 215 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 216 through 350 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 351 through 383 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 384 through 469 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 502 through 502 )

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 7 types, 1169 molecules

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Structure viewers

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Open data

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 7 types, 1169 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Yorodumi