PDB-7zd7: Crystal structure of the R24E/E352T double mutant of S-adenosyl-L...

ID or keywords:

Entry

Database: PDB / ID: 7zd7

Title

Crystal structure of the R24E/E352T double 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: 1.9 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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PDBx/mmCIF format	7zd7.cif.gz	346.5 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7zd7_validation.pdf.gz	2.2 MB	Display	wwPDB validaton report
Full document	7zd7_full_validation.pdf.gz	2.2 MB	Display
Data in XML	7zd7_validation.xml.gz	35.2 KB	Display
Data in CIF	7zd7_validation.cif.gz	52.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zd/7zd7 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zd7	HTTPS FTP

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Related structure data

Related structure data	7o5lSC 7o5mC 7zd8C 7zd9C 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

95 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&software
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)	120.897, 196.825, 81.920
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-848- HOH

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Protein , 1 types, 2 molecules AC

#1: Protein	Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 46210.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: ahcY, sll1234 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P74008, adenosylhomocysteinase

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Non-polymers , 6 types, 543 molecules

#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: 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
#4: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄ / Feature type: SUBJECT OF INVESTIGATION
#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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 530 / 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 plate
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 6.5 Details: 0.2 M sodium fluoride, 0.1 M Bis Tris propane pH 6.5, 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 19, 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: 1.9→103.015 Å / Num. obs: 148451 / % possible obs: 99.8 % / Redundancy: 6.914 % / B_iso Wilson estimate: 35.98 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.116 / R_rim(I) all: 0.125 / Χ²: 0.806 / Net I/σ(I): 11.11 / Num. measured all: 1026447

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
1.9-2.02	6.903	1.621	1.08	163832	24080	23733	0.474	1.752	98.6
2.02-2.15	6.679	0.954	1.98	151503	22685	22684	0.747	1.035	100
2.15-2.33	6.709	0.565	3.49	141186	21044	21044	0.893	0.613	100
2.33-2.55	7.027	0.344	5.82	135722	19315	19314	0.961	0.372	100
2.55-2.85	7.03	0.212	9.1	123222	17527	17527	0.984	0.229	100
2.85-3.29	6.739	0.115	15.5	104442	15498	15498	0.994	0.125	100
3.29-4.03	7.428	0.062	29.32	96682	13016	13016	0.998	0.067	100
4.03-5.69	7.104	0.046	38.19	71722	10096	10096	0.998	0.05	100
5.69-103.015	6.885	0.036	40.76	38136	5544	5539	0.999	0.039	99.9

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Processing

Software

Name	Version	Classification
XDS	1.19.2-4158	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: 1.9→51.51 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.24 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2001	1937	1.31 %
R_work	0.1659	146487	-
obs	0.1664	148424	99.75 %

Solvent computation

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

Displacement parameters

B_iso max: 96.93 Å² / B_iso mean: 39.7008 Å² / B_iso min: 23.5 Å²

Refinement step

Cycle: final / Resolution: 1.9→51.51 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6320	0	156	538	7014
B_iso mean	-	-	36.04	46.24	-
Num. residues	-	-	-	-	828

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 (%)
1.9-1.95	0.3265	134	0.3142	10208	10342	97
1.95-2	0.2714	137	0.2725	10474	10611	100
2-2.06	0.3082	139	0.2657	10482	10621	100
2.06-2.13	0.3007	135	0.239	10415	10550	100
2.13-2.2	0.2087	141	0.2124	10511	10652	100
2.2-2.29	0.2288	139	0.1865	10512	10651	100
2.29-2.39	0.2363	138	0.1815	10484	10622	100
2.39-2.52	0.2233	140	0.1665	10488	10628	100
2.52-2.68	0.2201	136	0.1798	10488	10624	100
2.68-2.88	0.2152	139	0.1624	10507	10646	100
2.89-3.18	0.1882	139	0.1749	10480	10619	100
3.18-3.63	0.2023	142	0.1476	10470	10612	100
3.64-4.58	0.1529	141	0.1253	10498	10639	100
4.58-51.51	0.1801	137	0.1517	10470	10607	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	2.0612	0.7803	-0.7072	1.7925	-0.0741	4.0352	-0.0408	-0.2164	0.0003	0.0414	-0.0207	-0.1713	-0.3187	0.273	0.0677	0.1963	0.0226	-0.0034	0.3152	0.0181	0.3252	26.4533	29.72	1.9958
2	1.444	1.2858	-0.2472	2.8351	0.0653	2.0333	-0.1405	0.0572	-0.119	-0.19	0.1129	0.0318	0.0615	0.0714	0.0239	0.2853	0.0304	0.0481	0.2846	0.0259	0.3069	17.5938	21.0031	-5.8317
3	0.8559	-0.4568	-0.1419	1.4879	-0.0636	0.5712	-0.0435	-0.0365	-0.1559	0.0365	-0.0423	-0.0308	0.0995	-0.0094	0.0896	0.2372	-0.0061	0.0046	0.2672	0.0125	0.2591	3.2119	27.2657	6.1665
4	1.8137	-0.0021	0.2964	2.4949	-1.3096	5.2876	0.0221	0.1935	-0.0586	-0.2908	-0.0428	0.028	0.0388	-0.087	0.0048	0.2069	0.014	-0.0296	0.2825	-0.0317	0.2708	-8.6027	35.9504	-1.0709
5	1.6876	-0.7059	0.242	1.5538	-0.5227	0.8164	0.0388	-0.0084	-0.1254	-0.1552	-0.0978	0.0455	0.1861	0.0428	0.0672	0.2675	0.0109	0.0249	0.2748	-0.0017	0.2339	9.6345	27.1188	4.8544
6	3.9727	3.809	-2.7997	5.0731	-3.8812	3.7448	0.297	-0.4306	-0.3595	0.2847	-0.499	-0.3866	-0.0545	0.5266	0.2081	0.3298	0.0418	0.0053	0.3233	0.0315	0.4045	12.0161	23.1712	36.8754
7	3.4607	0.0229	-2.0645	1.9084	1.5745	3.0215	0.0394	0.4849	-0.0282	-0.3501	-0.17	-0.0262	0.0082	-0.1281	0.1192	0.3837	0.0583	-0.0231	0.3995	0.0859	0.2822	3.3683	62.8497	-11.6564
8	2.1312	0.3267	-0.1887	2.7988	0.8775	1.8591	0.0453	0.2078	0.2479	-0.1691	0.0149	-0.3563	-0.2763	0.1814	-0.0531	0.4159	-0.0029	0.0624	0.4002	0.1001	0.3853	14.6486	71.1748	-7.6836
9	0.9029	-0.3532	-0.0015	1.1199	-0.0817	0.8767	0.0418	0.0121	0.1886	-0.0187	-0.0613	-0.0184	-0.1972	0.0498	0.0243	0.2832	-0.0253	0.0053	0.2787	0.0086	0.289	12.7464	62.5025	14.3386
10	7.7804	-2.9187	0.4056	5.1801	-0.2235	1.5431	0.1053	0.0149	0.2626	-0.2018	-0.0538	-0.3673	-0.0043	0.2297	-0.0404	0.2695	-0.0434	0.0202	0.3224	-0.0016	0.2368	28.4375	55.5668	12.7559
11	7.4057	-5.1286	5.3857	7.1662	-3.5998	6.1492	0.2551	0.4215	-0.209	-0.3416	-0.0973	-0.0222	0.1992	0.182	-0.153	0.2883	-0.0309	0.0321	0.3931	0.0056	0.2576	29.4389	47.9319	8.5982
12	2.7972	-1.5426	0.6681	4.7708	0.163	1.7628	0.1701	0.111	0.3222	-0.3971	-0.1477	0.007	-0.1975	-0.0031	-0.0153	0.3161	0.0092	0.0377	0.3044	0.0569	0.2567	5.5839	66.5193	0.9235
13	2.2426	0.678	-0.8785	0.4321	0.2004	1.2766	0.1299	0.2118	0.5218	0.024	0.0323	0.0594	-0.3477	-0.1692	-0.1906	0.4112	0.0959	-0.0091	0.3068	0.0618	0.4212	-11.2148	73.4874	10.6311

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 143 )	A	46 - 143
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 144 through 246 )	A	144 - 246
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 247 through 321 )	A	247 - 321
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 322 through 402 )	A	322 - 402
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 403 through 422 )	A	403 - 422
7	X-RAY DIFFRACTION	7	chain 'C' and (resid 9 through 45 )	C	9 - 45
8	X-RAY DIFFRACTION	8	chain 'C' and (resid 46 through 143 )	C	46 - 143
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 144 through 284 )	C	144 - 284
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 285 through 321 )	C	285 - 321
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 322 through 343 )	C	322 - 343
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 344 through 375 )	C	344 - 375
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 376 through 421 )	C	376 - 421

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