PDB-7zd9: Crystal structure of the E352T mutant of S-adenosyl-L-homocystein...

ID or keywords:

Entry

Database: PDB / ID: 7zd9

Title

Crystal structure of the E352T mutant of S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803 cocrystallized with adenosine in the presence of Rb+ cations

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS / MUTAGENESIS

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

Synechocystis sp. PCC 6803 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

Authors

Malecki, P.H. / Imiolczyk, B. / Wozniak, K. / Brzezinski, K.

Funding support

Poland, 1items

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Biochemical and structural insights into an unusual, alkali-metal-independent S-adenosyl-L-homocysteine hydrolase from Synechocystis sp. PCC 6803.
Authors: Malecki, P.H. / Imiolczyk, B. / Barciszewski, J. / Czyrko-Horczak, J. / Sliwiak, J. / Gawel, M. / Wozniak, K. / Jaskolski, M. / Brzezinski, K.

History

Deposition	Mar 29, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 13, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jan 31, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7zd9.cif.gz	349.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7zd9.ent.gz	280.5 KB	Display	PDB format
PDBx/mmJSON format	7zd9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7zd9_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	7zd9_full_validation.pdf.gz	2.4 MB	Display
Data in XML	7zd9_validation.xml.gz	37.5 KB	Display
Data in CIF	7zd9_validation.cif.gz	57.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zd/7zd9 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zd9	HTTPS FTP

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Related structure data

Related structure data	7o5lSC 7o5mC 7zd7C 7zd8C S: Starting model for refinement C: citing same article (ref.)
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	#118 - Oct 2009 Sodium-Potassium Pump similarity (1) #265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

A: Adenosylhomocysteinase

C: Adenosylhomocysteinase

hetero molecules

94.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenosylhomocysteinase

C: Adenosylhomocysteinase

hetero molecules

A: Adenosylhomocysteinase

C: Adenosylhomocysteinase

hetero molecules

defined by author
Evidence: gel filtration
190 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	121.117, 196.155, 81.638
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-907- HOH
2	1	A-1007- HOH

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Protein , 1 types, 2 molecules AC

#1: Protein	Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 46238.742 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: ahcY, sll1234 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P74008, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase

Mass: 46238.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Kazusa / Gene: ahcY, sll1234 / Production host:

Escherichia coli BL21 (bacteria) / References: UniProt: P74008, adenosylhomocysteinase

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Non-polymers , 6 types, 763 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-RB / RUBIDIUM ION Mass: 85.468 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54 % / Description: 2D plates
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 0.2 M Sodium formate pH 7.0, 20% w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

PETRA III, EMBL c/o DESY

/ Beamline: P13 (MX1) / Wavelength: 0.8146 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 12, 2022

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.8146 Å / Relative weight: 1

Reflection

Resolution: 1.89→81.638 Å / Num. obs: 150834 / % possible obs: 99.8 % / Redundancy: 6.829 % / B_iso Wilson estimate: 28.36 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.216 / R_rim(I) all: 0.234 / Χ²: 0.746 / Net I/σ(I): 9.27 / Num. measured all: 1030038

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.89-2	6.752	1.85	1.33	163291	24472	24183	0.511	2.003	98.8
2-2.14	6.596	1.239	2.34	151593	22985	22984	0.761	1.346	100
2.14-2.31	6.549	0.821	3.78	139870	21359	21359	0.882	0.892	100
2.31-2.53	6.963	0.557	5.73	137083	19686	19686	0.951	0.602	100
2.53-2.83	6.972	0.374	8.31	124004	17786	17786	0.977	0.404	100
2.83-3.27	6.721	0.211	12.94	105437	15687	15687	0.99	0.229	100
3.27-4	7.39	0.105	22.51	97796	13234	13234	0.996	0.113	100
4-5.64	7.084	0.075	28.54	72639	10254	10254	0.997	0.081	100
5.64-81.638	6.77	0.053	31.2	38325	5668	5661	0.999	0.057	99.9

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19.2-4158	refinement
PDB_EXTRACT	3.27	data extraction
REFMAC		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7O5L

7o5l

Resolution: 1.89→47.03 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 23.67 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2026	1946	1.29 %
R_work	0.1689	148844	-
obs	0.1693	150790	99.78 %

Solvent computation

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

Displacement parameters

B_iso max: 82.99 Å² / B_iso mean: 29.2558 Å² / B_iso min: 14.1 Å²

Refinement step

Cycle: final / Resolution: 1.89→47.03 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6358	0	137	766	7261
B_iso mean	-	-	23.04	37.12	-
Num. residues	-	-	-	-	834

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.89-1.93	0.4672	135	0.439	10384	10519	97
1.93-1.99	0.4028	143	0.3529	10679	10822	100
1.99-2.05	0.3266	139	0.2667	10608	10747	100
2.05-2.11	0.2495	140	0.2286	10632	10772	100
2.11-2.19	0.2395	140	0.2125	10616	10756	100
2.19-2.27	0.228	139	0.2	10719	10858	100
2.27-2.38	0.235	139	0.1917	10627	10766	100
2.38-2.5	0.2209	137	0.1572	10654	10791	100
2.5-2.66	0.19	140	0.1612	10659	10799	100
2.66-2.87	0.202	140	0.1535	10635	10775	100
2.87-3.15	0.1888	138	0.1587	10632	10770	100
3.15-3.61	0.1718	140	0.1393	10696	10836	100
3.61-4.55	0.147	139	0.1213	10662	10801	100
4.55-47.03	0.1666	137	0.1469	10641	10778	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	1.5164	0.8631	-0.5635	1.7069	-0.536	2.4583	-0.0076	-0.1531	-0.0811	0.0177	-0.0732	-0.1876	-0.055	0.2717	0.0694	0.1489	0.0271	0.0063	0.2322	0.0049	0.2435	26.3086	29.2585	1.7761
2	1.1848	0.7819	0.0205	1.3544	-0.6653	2.6059	-0.0687	0.0219	-0.234	-0.1325	0.0071	-0.1297	0.1038	0.2	0.0568	0.1776	0.0245	0.053	0.1787	0.0091	0.2029	20.8981	23.9558	-4.3069
3	2.3224	1.8372	-0.3478	4.3872	-1.2721	4.5129	-0.2612	0.1382	-0.14	-0.1672	0.1439	0.051	0.2392	-0.1882	0.1061	0.2379	0.0178	0.0526	0.1715	-0.0031	0.2427	11.4965	15.3627	-9.2045
4	0.7451	-0.4654	-0.2976	1.7665	0.0416	0.9589	-0.0537	-0.0282	-0.1985	-0.0159	-0.0454	0.0681	0.1589	0.0161	0.1026	0.1592	0.0004	0.0129	0.1796	0.0113	0.192	5.0056	24.1314	4.5195
5	1.6893	1.451	-0.3682	3.3421	-0.1794	0.281	0.0811	-0.1802	-0.0178	0.1355	-0.1696	-0.0653	-0.012	-0.0239	0.0913	0.209	0.0162	-0.0018	0.256	0.005	0.1518	-3.6021	37.5499	11.4074
6	1.7691	0.0036	-0.0623	1.7161	-0.6632	3.1928	0.0218	0.249	-0.0667	-0.2397	-0.033	0.1085	0.0604	-0.0995	0.0086	0.1636	0.0089	-0.0242	0.202	-0.0323	0.1701	-9.1999	36.1441	-0.9148
7	1.587	-1.002	0.4634	1.8654	-0.7349	0.8407	0.0741	0.0978	-0.0328	-0.1728	-0.1192	0.0571	0.0619	0.0239	0.0482	0.2091	0.0106	0.0159	0.2315	-0.0125	0.1675	6.7625	32.9831	-1.1753
8	1.2308	2.4748	1.5547	6.3952	3.296	3.2587	0.1335	-0.1285	-0.2641	0.385	-0.0872	-0.2082	0.4391	-0.0157	-0.0436	0.2607	0.0503	0.0388	0.2898	0.0653	0.2875	15.1316	15.4128	16.0562
9	2.5073	2.4789	-0.0579	4.5142	-1.8872	1.6333	0.5125	-0.4415	-0.2857	0.5282	-0.4465	0.0721	-0.0657	0.3228	-0.0437	0.2645	0.0232	0.0138	0.2309	0.0357	0.3415	10.6925	22.0176	39.6462
10	1.9939	-0.1037	-0.7108	2.2392	1.197	2.4212	-0.0335	0.2226	0.0418	-0.2273	-0.0287	0.1242	-0.1329	-0.0349	0.053	0.2677	0.013	-0.0307	0.2917	0.0586	0.1973	3.6285	62.0985	-11.7742
11	1.7184	0.2524	-0.4165	2.4865	1.0924	1.7115	-0.0004	0.2182	0.2359	-0.1854	0.0889	-0.242	-0.3114	0.2263	-0.0782	0.2999	-0.0313	0.0285	0.3149	0.087	0.2623	14.6455	70.606	-7.8071
12	1.0639	-0.3227	0.0429	1.2801	-0.106	1.0538	-0.0019	0.0324	0.2183	-0.055	0.0062	-0.0373	-0.2183	-0.0031	-0.0013	0.1943	-0.0133	-0.0037	0.1803	0.0035	0.1755	11.1193	64.4928	10.5757
13	3.0594	-1.1144	-0.872	1.7731	0.7529	1.618	0.0177	-0.0148	0.1123	-0.0374	0.023	-0.1679	-0.0537	0.2214	-0.0422	0.1903	-0.0431	-0.0194	0.2335	0.0139	0.19	23.1405	55.1139	18.2381
14	4.0846	-0.4462	-0.053	3.0865	0.9266	0.2892	-0.0156	-0.0334	-0.0462	-0.1362	0.0757	-0.151	0.0141	0.0902	-0.0712	0.241	-0.0181	0.0229	0.2986	0.0064	0.2056	29.4651	47.6075	8.531
15	2.5166	-1.3973	0.1933	3.7591	0.3359	1.304	0.163	0.0434	0.2317	-0.2968	-0.1489	-0.0313	-0.1863	0.0246	0.0022	0.2424	-0.0119	0.0155	0.2331	0.04	0.1814	5.5928	66.0614	0.7931
16	1.7637	0.4453	-0.4821	0.7126	0.4031	1.4042	0.0593	0.1727	0.4505	-0.0024	0.0387	0.0354	-0.3275	-0.17	-0.1159	0.2853	0.0792	-0.0176	0.2092	0.0571	0.2958	-11.3442	73.1155	10.8903
17	8.5394	-1.7256	-2.9138	7.878	-7.3147	9.2906	-0.3012	-0.2165	0.0766	0.2303	-2.2995	-2.9237	1.5059	2.1182	2.5855	0.9482	0.098	-0.1154	0.8216	-0.0186	0.8204	-25.1199	71.2007	35.2935

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 9 through 45 )	A	9 - 45
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 46 through 110 )	A	46 - 110
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 111 through 143 )	A	111 - 143
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 144 through 223 )	A	144 - 223
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 224 through 246 )	A	224 - 246
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 247 through 321 )	A	247 - 321
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 322 through 375 )	A	322 - 375
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 376 through 402 )	A	376 - 402
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 403 through 425 )	A	403 - 425
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 9 through 45 )	C	9 - 45
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 46 through 143 )	C	46 - 143
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 144 through 246 )	C	144 - 246
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 247 through 321 )	C	247 - 321
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 322 through 343 )	C	322 - 343
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 344 through 375 )	C	344 - 375
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 376 through 422 )	C	376 - 422
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 423 through 425 )	C	423 - 425

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