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

ID or keywords:

Entry

Database: PDB / ID: 8cfb

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from P. aeruginosa in complex with F2X-Entry library fragment D02

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: 2.07 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 F2X-Entry library fragment D02
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	8cfb.cif.gz	739.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8cfb.ent.gz	617.1 KB	Display	PDB format
PDBx/mmJSON format	8cfb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8cfb_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	8cfb_full_validation.pdf.gz	2 MB	Display
Data in XML	8cfb_validation.xml.gz	70.2 KB	Display
Data in CIF	8cfb_validation.cif.gz	96.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/cf/8cfb ftp://data.pdbj.org/pub/pdb/validation_reports/cf/8cfb	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)	175.970, 103.680, 109.200
Angle α, β, γ (deg.)	90.00, 99.99, 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) / 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, 545 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-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#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-SY4 / ~{N}-[5-azanyl-2,4-bis(fluoranyl)phenyl]propane-1-sulfonamide Mass: 250.266 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₂F₂N₂O₂S / Feature type: SUBJECT OF INVESTIGATION
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.37 Å³/Da / Density % sol: 48.11 %
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: 2.07→48.6 Å / Num. obs: 224478 / % possible obs: 96.7 % / Redundancy: 2.34 % / CC_1/2: 0.996 / R_merge(I) obs: 0.097 / R_rim(I) all: 0.124 / Net I/σ(I): 7.15

Reflection shell

Resolution (Å)	R_merge(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	Diffraction-ID
2.07-2.19	1.478	35326	0.288	1.895	1
2.19-2.34	0.853	34305	0.52	1.097	1
2.34-2.53	0.523	31951	0.732	0.673	1
2.53-2.77	0.334	29502	0.867	0.427	1
2.77-3.09	0.175	26568	0.96	0.224	1
3.09-3.57	0.087	23393	0.99	0.112	1
3.57-4.37	0.042	19756	0.997	0.054	1
4.37-6.15	0.03	15211	0.998	0.038	1
6.15-48.6	0.021	8466	0.999	0.026	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: 2.07→32.64 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 36.58 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.271	2097	1.79 %
R_work	0.2354	-	-
obs	0.236	117060	99.04 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.07→32.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14218	0	315	516	15049

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	14866
X-RAY DIFFRACTION	f_angle_d	0.525	20165
X-RAY DIFFRACTION	f_dihedral_angle_d	13.699	5498
X-RAY DIFFRACTION	f_chiral_restr	0.042	2253
X-RAY DIFFRACTION	f_plane_restr	0.003	2663

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 (%)
2.07-2.11	0.4796	127	0.4474	6932	X-RAY DIFFRACTION	90
2.11-2.17	0.4232	140	0.4033	7696	X-RAY DIFFRACTION	100
2.17-2.23	0.4284	141	0.3939	7683	X-RAY DIFFRACTION	100
2.23-2.29	0.391	139	0.3657	7700	X-RAY DIFFRACTION	100
2.29-2.37	0.374	141	0.3349	7682	X-RAY DIFFRACTION	100
2.37-2.45	0.4063	140	0.3345	7685	X-RAY DIFFRACTION	100
2.45-2.55	0.3276	142	0.3075	7758	X-RAY DIFFRACTION	100
2.55-2.66	0.3514	140	0.3051	7674	X-RAY DIFFRACTION	100
2.66-2.8	0.3764	141	0.2832	7711	X-RAY DIFFRACTION	100
2.8-2.98	0.3126	140	0.2632	7719	X-RAY DIFFRACTION	100
2.98-3.21	0.2854	142	0.2637	7748	X-RAY DIFFRACTION	100
3.21-3.53	0.2295	141	0.2257	7741	X-RAY DIFFRACTION	100
3.53-4.04	0.2031	140	0.1975	7687	X-RAY DIFFRACTION	99
4.04-5.09	0.2307	141	0.1679	7731	X-RAY DIFFRACTION	99
5.09-32.64	0.2178	142	0.1826	7816	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	1.4361	-0.4429	-0.5761	2.1002	-0.0982	1.5336	-0.1099	0.0716	-0.2306	-0.1351	0.0318	0.2457	0.2188	-0.4166	0.0691	0.3669	-0.1362	-0.0322	0.4924	-0.0347	0.3359	4.546	-0.4658	28.0426
2	1.3941	0.0257	-1.2045	1.1093	-0.7483	1.948	-0.0707	-0.0491	0.0599	0.1295	0.0997	0.0894	-0.0848	-0.331	-0.0359	0.3568	-0.0138	-0.0703	0.4713	-0.0586	0.3606	5.0743	10.4162	39.1519
3	1.7083	-0.2258	0.3983	2.5624	0.1349	2.3898	-0.104	0.0165	0.5528	0.031	0.0022	-0.5228	-0.2765	-0.2003	0.1015	0.3068	0.0251	-0.0465	0.3164	-0.0102	0.5355	20.1033	27.9996	27.4832
4	2.9091	-0.4231	-0.291	2.331	-0.203	1.1464	-0.1369	-0.4703	0.0438	0.4677	0.1906	-0.2642	0.2434	-0.1519	-0.0352	0.4179	-0.0073	-0.0766	0.3708	0.0054	0.3216	19.5481	-2.5038	47.3672
5	2	2	2	2	2	2	0.4528	-1.0821	1.6871	0.3255	-2.2938	1.9371	1.4073	-0.5925	1.8425	0.4669	-0.052	-0.0542	0.5139	-0.0418	0.4317	13.346	7.751	30.0078
6	4.3903	1.4681	-1.4963	4.711	0.6432	0.8284	-0.0848	0.7744	0.1846	-1.3478	-0.1375	-0.0354	-0.0232	-0.1698	0.2228	0.8885	0.0221	-0.0205	0.6658	0.0903	0.4512	13.598	22.5728	-0.3738
7	1.752	-0.3038	0.6924	0.1697	-0.906	5.7616	-0.0568	0.5606	0.869	-1.0832	-0.2646	-0.4259	-0.8087	0.1772	0.2449	1.2655	0.0812	0.3412	0.5529	0.2013	0.7781	28.78	28.9552	-5.7499
8	1.6612	-0.2726	0.0578	0.2527	-0.6872	2.2226	0.0644	0.7383	0.3161	-1.3844	-0.0869	-0.389	0.0433	-0.4371	0.0028	1.0245	0.0082	0.1627	0.6923	0.1381	0.4419	20.1728	18.4781	-4.9236
9	1.8424	0.3533	-0.6694	0.6321	0.7453	1.591	-0.0367	0.7217	-0.0725	-0.5868	-0.0941	-0.1437	0.3248	-0.2018	0.1213	1.9447	0.1354	0.4783	0.8193	0.0762	0.4354	25.3259	11.7883	-15.737
10	1.6602	0.6634	-0.9602	0.2951	-0.3224	1.4736	0.0818	0.3706	0.058	-1.1813	-0.279	-0.7903	-0.1008	0.2768	0.1266	1.2625	0.1636	0.5808	0.5704	0.1796	0.9099	36.3738	13.4079	-3.6038
11	2.4081	-0.1748	-0.8578	0.9688	-0.1284	1.9366	0.008	0.3067	0.2045	-0.6702	-0.1714	-1.1031	0.3396	0.0709	0.144	0.6023	0.0276	0.291	0.3905	0.0493	0.8061	39.4914	-1.3675	14.9539
12	1.8529	-1.4461	0.2827	2.9027	0.3876	2.1268	-0.0471	0.4608	-0.476	-0.7953	-0.131	-0.2321	0.5773	-0.168	0.1914	0.7202	-0.0859	0.2071	0.4997	-0.1089	0.5153	23.7219	-5.8072	8.7299
13	0.1795	0.0717	-0.3374	0.0304	-0.1471	0.6775	0.2205	0.1803	0.0205	-1.2709	-0.0351	-0.8504	-0.3059	0.449	-0.1937	1.4475	0.1187	0.7568	0.8092	0.2022	1.2807	39.9887	24.1391	-10.6269
14	0.8556	0.3605	-0.5695	0.1628	-0.1945	0.6662	-0.0579	0.1555	0.0864	-0.3934	-0.1755	-0.9376	-0.0826	0.3434	0.162	0.7258	0.0061	0.3656	0.6381	0.3084	1.712	48.9457	31.8072	8.1383
15	3.8641	-6.1499	-0.6871	2	2.0997	2.2892	0.9172	3.1732	1.6888	-0.5967	-3.0273	-1.3398	2.034	0.6018	2.1131	0.713	0.1547	0.2612	0.5891	-0.0421	0.7897	27.9138	15.6321	3.2542
16	1.0813	-0.1133	-0.4124	0.5132	0.2111	0.9897	-0.2274	-0.0823	0.2753	-0.0566	-0.1537	-0.5057	0.1963	0.708	-0.041	0.2942	0.278	0.2411	0.8688	0.3949	2.4651	75.7276	9.0728	25.4964
17	0.0907	0.0324	-0.2832	0.003	-0.1057	0.936	-0.1198	-0.029	0.506	-0.03	-0.1689	-0.7555	-0.1889	0.5717	0.0404	0.4763	0.0284	0.2895	0.8448	0.3489	2.4589	72.1862	20.7722	15.8985
18	0.2742	0.2294	-0.1362	0.4978	-0.2054	0.1489	-0.0874	0.0579	0.8344	-0.0609	-0.1829	-1.0643	-0.1966	0.2706	0.1376	0.4405	-0.1027	-0.0681	0.5118	0.148	2.101	51.7764	32.2881	27.3402
19	1.2825	0.1801	0.1091	0.2549	-0.4573	0.8353	-0.197	0.2748	0.3078	-0.2718	-0.2802	-0.978	0.1145	0.4476	0.265	0.5358	0.0956	0.4456	0.629	0.2404	2.0178	61.0365	12.8146	14.1848
20	2	-3.0557	5.7094	1.2962	0.8105	2	3.77	3.7204	-0.9276	-1.9428	-4.8171	-0.1196	0.1008	4.4096	1.0512	0.7037	0.2891	-0.1379	0.7342	0.1699	1.4079	64.97	14.7093	24.3303
21	2.4015	-0.4974	0.3087	1.0294	-0.8287	1.2564	-0.2556	-0.2711	0.3882	0.1146	-0.0711	0.1348	-0.175	0.1938	0.3216	0.7394	0.0181	-0.4658	0.7668	-0.2071	1.7387	61.2549	24.8209	56.6077
22	0.5346	-0.1091	0.3458	0.8321	0.0435	0.3868	-0.2022	-0.7291	0.6569	0.3515	0.0803	-0.1552	-0.1408	-0.2223	0.2011	0.9093	0.2519	-0.7148	0.9151	-0.478	1.4847	45.2091	25.9862	62.5722
23	0.8023	0.456	-0.2489	0.2618	-0.1221	1.2978	-0.1414	-0.4968	0.0979	0.1468	-0.1713	-0.1491	0.0068	0.3592	0.0428	0.7077	0.1514	-0.5756	0.814	-0.2992	1.7663	56.0956	18.5951	60.4318
24	2.8972	0.7971	0.644	0.8668	-0.5886	1.513	-0.2558	-1.3096	0.1684	0.6496	0.0638	-0.4234	0.2348	0.3075	0.1581	0.8788	0.2864	-0.4242	0.9649	-0.1906	0.9068	47.8914	8.1965	69.265
25	1.2336	0.024	0.8675	1.7211	-0.041	1.8363	-0.1762	-0.1674	0.4578	0.1868	0.0643	-0.835	-0.0156	0.0812	0.1144	0.3971	0.0516	-0.1406	0.3502	-0.0445	0.8287	41.4509	4.1183	41.3682
26	1.8716	0.1525	0.0154	0.0458	-0.1396	1.1178	-0.1752	-0.258	0.0759	0.2366	0.1083	-1.0728	0.277	0.3485	0.0735	0.609	0.1168	-0.1904	0.5236	-0.0135	1.3975	56.1217	-4.6309	42.391
27	3.225	-0.0039	1.7806	0.7455	0.6805	2.0166	-0.2765	-0.6549	0.5033	0.6664	0.292	-0.6611	0.0221	-0.1971	0.0065	0.6815	0.1746	-0.3058	0.5224	-0.2416	0.8234	30.225	22.1614	57.0203
28	2	7.7761	-7.0977	2	7.9424	2	1.4486	0.3171	-0.7805	0.9213	-0.767	-1.5264	0.8448	-0.6865	-0.691	0.5799	0.1286	-0.4512	0.5403	-0.1404	1.1284	49.4477	15.1825	51.2496

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 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 34 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 35 through 63 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 64 through 112 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 113 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 305 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 306 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 112 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 113 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 469 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 502 through 502 )
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 9 through 34 )
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 35 through 63 )
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 64 through 112 )
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 113 through 178 )
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 179 through 279 )
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 280 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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Non-polymers , 7 types, 545 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