PDB-7zd8: Crystal structure of the R24E mutant of S-adenosyl-L-homocysteine...

ID or keywords:

Entry

Database: PDB / ID: 7zd8

Title

Crystal structure of the R24E 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

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: 2.03 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

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	7zd8.cif.gz	341.5 KB	Display	PDBx/mmCIF format
PDB format	pdb7zd8.ent.gz	275.9 KB	Display	PDB format
PDBx/mmJSON format	7zd8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	7zd8_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	7zd8_full_validation.pdf.gz	2.3 MB	Display
Data in XML	7zd8_validation.xml.gz	35.1 KB	Display
Data in CIF	7zd8_validation.cif.gz	51.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zd/7zd8 ftp://data.pdbj.org/pub/pdb/validation_reports/zd/7zd8	HTTPS FTP

-
Related structure data

Related structure data	7o5lSC 7o5mC 7zd7C 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

-
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

95.1 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)	120.310, 195.837, 81.943
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

-
Protein , 1 types, 2 molecules AC

#1: Protein	Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 46238.676 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

-
Non-polymers , 6 types, 463 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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-RB / RUBIDIUM ION Mass: 85.468 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Rb / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 449 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54 % / Description: 2D plate
Crystal grow	Temperature: 291 K / Method: vapor diffusion / pH: 7 Details: 0.2 M sodium chloride, 0.1 M HEPES pH 7.0, 20 % w/v PEG 6000

-
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: 2.03→102.511 Å / Num. obs: 120727 / % possible obs: 99.8 % / Redundancy: 6.868 % / B_iso Wilson estimate: 41.4 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.124 / R_rim(I) all: 0.134 / Χ²: 0.794 / Net I/σ(I): 10.32 / Num. measured all: 829146

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
2.03-2.15	6.517	1.682	1.02	126042	19612	19340	0.592	1.826	98.6
2.15-2.3	6.605	1.005	1.76	121808	18442	18442	0.76	1.091	100
2.3-2.49	7.013	0.607	3.01	119874	17093	17092	0.903	0.655	100
2.49-2.72	6.994	0.383	4.78	110078	15740	15739	0.956	0.413	100
2.72-3.04	6.946	0.224	8.15	98883	14235	14235	0.984	0.242	100
3.04-3.51	6.866	0.113	15.37	86214	12556	12556	0.995	0.122	100
3.51-4.3	7.358	0.065	28.2	78181	10627	10626	0.998	0.07	100
4.3-6.08	6.88	0.053	33.44	56403	8199	8198	0.998	0.057	100
6.08-102.511	7.038	0.037	40.84	31663	4507	4499	0.999	0.04	99.8

-
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: 2.03→62.84 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.203	1939	1.61 %
R_work	0.1681	118683	-
obs	0.1687	120622	99.68 %

Solvent computation

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

Displacement parameters

B_iso max: 99.58 Å² / B_iso mean: 46.3685 Å² / B_iso min: 29.04 Å²

Refinement step

Cycle: final / Resolution: 2.03→62.84 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6341	0	157	456	6954
B_iso mean	-	-	42.92	51.18	-
Num. residues	-	-	-	-	831

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 (%)
2.03-2.08	0.3575	135	0.3264	8257	8392	97
2.08-2.14	0.2886	134	0.2858	8482	8616	100
2.14-2.2	0.3173	140	0.2811	8494	8634	100
2.2-2.27	0.2956	138	0.2524	8468	8606	100
2.27-2.35	0.3265	140	0.2327	8534	8674	100
2.35-2.45	0.2629	140	0.2081	8467	8607	100
2.45-2.56	0.258	135	0.1965	8493	8628	100
2.56-2.69	0.2086	139	0.1864	8480	8619	100
2.69-2.86	0.1931	140	0.1846	8507	8647	100
2.86-3.08	0.2334	141	0.1656	8528	8669	100
3.08-3.39	0.2171	140	0.1661	8484	8624	100
3.39-3.88	0.185	139	0.1328	8487	8626	100
3.88-4.89	0.16	139	0.1249	8507	8646	100
4.89-62.84	0.1503	139	0.1534	8495	8634	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	1.7768	0.9011	-1.0545	1.6606	-0.0649	2.3213	-0.0204	-0.2235	-0.1599	0.0638	-0.1034	-0.2297	-0.1376	0.3277	0.1159	0.3034	0.03	-0.0159	0.4491	0.0448	0.4139	26.3207	29.4854	1.833
2	1.4544	1.1912	0.0437	1.351	0.0551	2.6729	-0.1059	0.0366	-0.1515	-0.0741	0.0651	-0.129	0.047	0.1783	0.0313	0.3463	0.0346	0.0592	0.3438	0.0202	0.3935	20.842	23.9323	-4.1915
3	3.0151	2.7568	0.1302	4.7833	-2.2291	7.2455	-0.2013	0.1863	-0.0118	-0.2453	0.1377	0.0452	0.1433	-0.2256	0.0637	0.371	0.0259	0.0735	0.3215	0.0074	0.4324	11.3291	15.4277	-9.0932
4	1.0749	0.3871	0.2023	3.6496	1.2135	1.5602	-0.0314	-0.1276	-0.3173	-0.0887	-0.1483	0.125	0.2163	-0.05	0.1766	0.4008	0.0165	0.0445	0.3919	0.0488	0.4542	6.6983	14.7311	4.3931
5	1.345	0.5922	-0.4129	2.0149	-0.6182	1.6929	0.0076	-0.0944	-0.0412	0.0203	-0.0497	0.0823	-0.0729	-0.1785	0.0431	0.2693	0.025	-0.0113	0.3212	-0.0206	0.292	-5.9417	38.7364	5.6505
6	2.123	1.1432	0.2411	6.1999	-2.2935	4.552	0.0319	0.1783	-0.1356	-0.6208	0.011	-0.104	0.425	0.1571	-0.0527	0.3873	0.0592	0.0031	0.4967	-0.0775	0.3799	-4.3572	36.1419	-10.9879
7	8.3801	-3.4978	5.6076	3.5422	-2.1	6.1504	0.1378	0.3441	0.008	-0.3991	-0.1399	0.0582	0.1761	0.0805	-0.0015	0.3709	-0.0224	0.0146	0.3271	-0.0074	0.2994	0.3521	40.4203	-7.2458
8	0.904	0.7818	0.3658	4.6451	1.4627	2.2468	-0.0627	-0.2752	-0.2768	0.1296	-0.0239	-0.129	0.3369	0.0997	0.0812	0.3442	0.06	0.0517	0.4213	0.0871	0.4028	16.1451	17.4309	13.5561
9	3.8815	4.0012	-0.694	7.385	-2.9432	1.6372	0.5431	-0.6817	-0.2827	0.6777	-0.4276	0.2429	-0.141	0.2311	-0.1003	0.3642	0.02	-0.0025	0.3492	0.0429	0.4313	10.7888	22.2454	39.7249
10	1.5255	0.2128	-0.1497	2.084	0.5508	1.7341	0.037	0.1552	0.1253	-0.2342	0.0202	-0.2392	-0.2808	0.1595	-0.0558	0.4136	0.0209	0.0275	0.4037	0.072	0.4	11.1604	71.095	-4.5093
11	2.3758	-0.5223	-0.4921	1.7182	0.877	1.6482	-0.0033	-0.0578	0.08	-0.0276	0.0161	-0.0775	-0.0347	0.1567	-0.0102	0.3049	-0.0249	-0.007	0.3432	0.034	0.2897	20.1363	52.8821	15.7334
12	2.2427	-0.2956	-0.9245	0.4502	0.2518	0.9726	0.0915	0.0391	0.3107	-0.076	0.0038	0.0367	-0.3023	-0.0738	-0.1111	0.4396	0.0444	-0.0152	0.3741	0.0305	0.3994	-4.7217	70.6868	7.021

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 193 )	A	144 - 193
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 194 through 299 )	A	194 - 299
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 300 through 323 )	A	300 - 323
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 324 through 355 )	A	324 - 355
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 356 through 402 )	A	356 - 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 193 )	C	9 - 193
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 194 through 343 )	C	194 - 343
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 344 through 422 )	C	344 - 422

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AC

-
Non-polymers , 6 types, 463 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Protein , 1 types, 2 molecules AC

-Non-polymers , 6 types, 463 molecules

-Details

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 2 molecules AC

-
Non-polymers , 6 types, 463 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi