PDB-8ajt: Crystal structure of the H323A mutant of S-adenosyl-L-homocystein...

ID or keywords:

Entry

Database: PDB / ID: 8ajt

Title

Crystal structure of the H323A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / REGULATION OF SAM-DEPENDENT METHYLATION REACTIONS

Function / homology

Function and homology information

adenosylhomocysteinase / S-adenosylmethionine cycle /

adenosylhomocysteinase activity / one-carbon metabolic process /

cytosol
Similarity search - Function

Biological species

Pseudomonas aeruginosa PAO1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.499 Å

Authors

Drozdzal, P. / Wozniak, K. / Malecki, P. / Gawel, M. / Komorowska, M. / Brzezinski, K.

Funding support

Poland, 1items

Citation

Journal: To Be Published
Title: Crystal structure of the H323A mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations
Authors: Drozdzal, P. / Wozniak, K. / Malecki, P. / Gawel, M. / Komorowska, M. / Brzezinski, K.

History

Deposition	Jul 28, 2022	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 16, 2023	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ajt.cif.gz	712.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8ajt.ent.gz		Display	PDB format
PDBx/mmJSON format	8ajt.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/8ajt ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8ajt	HTTPS FTP

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Related structure data

Related structure data	6f3mS 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	#265 - Jan 2022 Golgi Casein Kinase similarity (1)

Deposited unit

AAA: Adenosylhomocysteinase

BBB: Adenosylhomocysteinase

CCC: Adenosylhomocysteinase

DDD: Adenosylhomocysteinase

hetero molecules

213 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: native gel electrophoresis

Unit cell

Length a, b, c (Å)	176.710, 134.561, 108.091
Angle α, β, γ (deg.)	90.000, 105.713, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	BBB-506- CL

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	BBB
3	2	AAA
4	2	CCC
5	3	AAA
6	3	DDD
7	4	BBB
8	4	CCC
9	5	BBB
10	5	DDD
11	6	CCC
12	6	DDD

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 9 - 469 / Label seq-ID: 12 - 472

Dom-ID	Component-ID	Ens-ID	Auth asym-ID	Label asym-ID
1	1	1	AAA	A
2	2	1	BBB	B
3	3	2	AAA	A
4	4	2	CCC	C
5	5	3	AAA	A
6	6	3	DDD	D
7	7	4	BBB	B
8	8	4	CCC	C
9	9	5	BBB	B
10	10	5	DDD	D
11	11	6	CCC	C
12	12	6	DDD	D

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein	Adenosylhomocysteinase / / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 51667.965 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / 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: 51667.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / 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 , 8 types, 1614 molecules

#2: Chemical	ChemComp-ADN / ADENOSINE / Adenosine Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#7: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#8: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1575 / 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: 2.99 Å³/Da / Density % sol: 58.9 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: Morpheus Crystallization Screen, Condition C12

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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: 0.97625 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.46→42.559 Å / Num. obs: 826623 / % possible obs: 98.9 % / Redundancy: 3.372 % / CC_1/2: 0.999 / Net I/σ(I): 8.88
Reflection shell	Resolution: 1.46→1.55 Å / Mean I/σ(I) obs: 0.53 / Num. unique obs: 128876 / CC_1/2: 0.316

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6F3M

6f3m

Resolution: 1.499→42.559 Å / Cor.coef. F_o:F_c: 0.983 / Cor.coef. F_o:F_c free: 0.976 / SU B: 3.384 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.052 / ESU R Free: 0.052 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.167	1045	0.27 %
R_work	0.1521	385919	-
all	0.152	-	-
obs	-	386964	99.832 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK

Displacement parameters

B_iso mean: 30.664 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.015 Å²	-0 Å²	-0.809 Å²
2-	-	-0.651 Å²	0 Å²
3-	-	-	1.831 Å²

Refinement step

Cycle: LAST / Resolution: 1.499→42.559 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14188	0	379	1575	16142

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.013	15092
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14420
X-RAY DIFFRACTION	r_angle_refined_deg	1.485	1.637	20516
X-RAY DIFFRACTION	r_angle_other_deg	1.433	1.584	33237
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.375	5	1918
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.417	23.611	709
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.099	15	2601
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.182	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.085	0.2	2007
X-RAY DIFFRACTION	r_gen_planes_refined	0.013	0.02	17234
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	3250
X-RAY DIFFRACTION	r_nbd_refined	0.225	0.2	3128
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.182	0.2	13720
X-RAY DIFFRACTION	r_nbtor_refined	0.166	0.2	7329
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	6661
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.145	0.2	1301
X-RAY DIFFRACTION	r_metal_ion_refined	0.116	0.2	10
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.286	0.2	18
X-RAY DIFFRACTION	r_nbd_other	0.219	0.2	50
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.139	0.2	22
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined	0.065	0.2	3
X-RAY DIFFRACTION	r_mcbond_it	1.281	1.713	7556
X-RAY DIFFRACTION	r_mcbond_other	1.27	1.712	7553
X-RAY DIFFRACTION	r_mcangle_it	1.742	2.565	9485
X-RAY DIFFRACTION	r_mcangle_other	1.742	2.564	9486
X-RAY DIFFRACTION	r_scbond_it	2.409	2.007	7536
X-RAY DIFFRACTION	r_scbond_other	2.377	2.002	7527
X-RAY DIFFRACTION	r_scangle_it	3.466	2.919	11024
X-RAY DIFFRACTION	r_scangle_other	3.451	2.913	11013
X-RAY DIFFRACTION	r_lrange_it	5.702	35.649	69018
X-RAY DIFFRACTION	r_lrange_other	5.513	34.673	67335
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.07	0.05	15487
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.051	0.05	15719
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.058	0.05	15593
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.066	0.05	15502
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.062	0.05	15483
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.064	0.05	15517

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	AAA	X-RAY DIFFRACTION	Local ncs	0.06977	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.06977	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.05119	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.05119	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.05825	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.05825	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.06644	0.05009
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.06644	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.06174	0.05009
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.06174	0.05009
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.06362	0.05009
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.06362	0.05009

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.499-1.538	0.479	75	0.505	27917	0.505	28509	0.027	0.06	98.1865	0.5
1.538-1.58	0.388	76	0.412	27805	0.412	27883	0.44	0.373	99.9928	0.397
1.58-1.626	0.329	73	0.345	27020	0.345	27094	0.554	0.59	99.9963	0.323
1.626-1.676	0.305	71	0.281	26271	0.281	26344	0.722	0.743	99.9924	0.253
1.676-1.731	0.193	69	0.229	25430	0.229	25505	0.878	0.845	99.9765	0.199
1.731-1.791	0.183	66	0.204	24624	0.203	24697	0.908	0.897	99.9717	0.173
1.791-1.859	0.19	65	0.18	23760	0.18	23834	0.931	0.93	99.9622	0.149
1.859-1.935	0.163	62	0.155	22873	0.155	22937	0.948	0.954	99.9913	0.131
1.935-2.021	0.166	59	0.146	21954	0.146	22015	0.955	0.962	99.9909	0.126
2.021-2.119	0.17	57	0.142	20954	0.142	21012	0.965	0.966	99.9952	0.126
2.119-2.233	0.166	54	0.136	19926	0.136	19982	0.969	0.97	99.99	0.124
2.233-2.368	0.178	51	0.126	18963	0.127	19019	0.965	0.976	99.9737	0.119
2.368-2.531	0.148	48	0.119	17723	0.119	17777	0.975	0.98	99.9662	0.114
2.531-2.733	0.142	45	0.121	16497	0.121	16564	0.978	0.98	99.8672	0.119
2.733-2.993	0.114	41	0.124	15278	0.124	15320	0.982	0.98	99.9935	0.127
2.993-3.344	0.159	37	0.136	13815	0.136	13858	0.975	0.978	99.9567	0.144
3.344-3.858	0.138	33	0.125	12168	0.125	12211	0.978	0.981	99.9181	0.14
3.858-4.715	0.119	28	0.109	10320	0.109	10363	0.98	0.984	99.8553	0.132
4.715-6.627	0.155	22	0.151	8045	0.151	8075	0.97	0.975	99.9009	0.182
6.627-42.559	0.233	13	0.181	4577	0.181	4597	0.963	0.97	99.8477	0.233

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	2.2769	0.0639	-0.5813	1.067	0.0344	0.6976	0.0269	-0.0575	0.3253	0.0018	0.0158	-0.1091	-0.1629	0.0843	-0.0427	0.1041	-0.0614	-0.0709	0.0499	0.0035	0.238	49.1297	34.0504	34.8865
2	1.116	-0.0774	0.0206	0.7217	0.3912	0.5667	-0.0027	0.1912	0.1206	-0.2135	0.0062	-0.035	-0.1577	0.0433	-0.0035	0.1185	-0.0449	-0.0563	0.0656	0.0532	0.1207	37.3251	17.6679	15.0845
3	0.5626	0.1707	-0.2859	0.8981	0.1778	0.368	0.048	0.0112	0.0594	-0.0903	-0.006	-0.1149	-0.0904	0.0676	-0.042	0.0786	-0.0414	-0.0453	0.0604	0.0297	0.1394	45.9752	19.519	27.9247
4	1.5842	0.29	-0.3323	1.2016	-0.0974	0.9809	-0.0168	-0.0379	0.3483	0.0603	-0.0252	0.339	-0.2678	-0.2419	0.042	0.1335	0.0594	-0.0963	0.0884	-0.0177	0.349	1.2057	30.6706	30.5765
5	1.1755	0.1956	0.3116	1.4139	-0.0745	0.8845	0.0238	-0.1201	0.0811	0.1518	-0.0367	0.1321	-0.0165	-0.1041	0.0129	0.0502	-0.0163	-0.034	0.0298	-0.002	0.1052	16.5588	9.7953	42.1423
6	0.5906	0.294	0.5167	0.8063	0.5606	1.2011	-0.0267	-0.0913	0.1756	-0.0044	-0.0744	0.2441	-0.0779	-0.2382	0.1011	0.0515	0.0034	-0.0508	0.0607	0.0077	0.1932	6.866	15.6269	31.3165
7	2.2277	-0.1024	0.0443	1.1713	0.189	0.5101	0.0069	0.0166	-0.285	-0.0058	-0.0381	0.1286	0.1655	-0.0785	0.0312	0.0907	-0.0478	-0.0542	0.0292	0.0259	0.1931	7.3969	-29.7023	28.0825
8	0.8476	-0.0965	-0.0706	0.7421	-0.3219	0.8134	-0.0082	0.1363	-0.0373	-0.0749	-0.0132	0.0857	0.0277	-0.0223	0.0214	0.0575	-0.0239	-0.0732	0.0431	0.0132	0.1079	14.4761	-6.4497	13.7554
9	0.7005	0.1446	0.2512	0.8567	-0.0817	0.1933	0.0378	0.016	-0.0476	0.0099	-0.0319	0.176	0.0482	-0.0344	-0.0058	0.0653	-0.0446	-0.0536	0.0413	0.0046	0.1631	9.6215	-13.8295	26.4571
10	1.6777	0.2065	0.2537	1.4388	0.199	0.9342	0.0127	0.2358	-0.248	-0.0919	0.0364	-0.3027	0.1979	0.2723	-0.0491	0.1022	0.0206	-0.0148	0.1635	-0.0374	0.232	52.7136	-22.4486	12.0847
11	1.1233	0.2463	-0.1514	1.1864	0.1288	1.0249	0.0315	-0.0672	-0.0962	0.0899	-0.0154	-0.1764	0.0509	0.143	-0.0161	0.0473	-0.0154	-0.0765	0.0321	0.0363	0.1298	42.3855	-8.4631	34.5304
12	0.6447	0.148	-0.219	1.0133	-0.2975	0.8808	-0.0069	0.0425	-0.1036	-0.1085	-0.0364	-0.248	0.0223	0.2296	0.0434	0.0516	-0.0169	-0.0364	0.0921	0.0151	0.1719	47.9172	-9.2871	20.2193

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	9 - 169
2	X-RAY DIFFRACTION	2	ALL	AAA	170 - 331
3	X-RAY DIFFRACTION	3	ALL	AAA	332 - 469
4	X-RAY DIFFRACTION	4	ALL	BBB	9 - 172
5	X-RAY DIFFRACTION	5	ALL	BBB	173 - 329
6	X-RAY DIFFRACTION	6	ALL	BBB	330 - 469
7	X-RAY DIFFRACTION	7	ALL	CCC	9 - 172
8	X-RAY DIFFRACTION	8	ALL	CCC	173 - 329
9	X-RAY DIFFRACTION	9	ALL	CCC	330 - 469
10	X-RAY DIFFRACTION	10	ALL	DDD	9 - 172
11	X-RAY DIFFRACTION	11	ALL	DDD	173 - 329
12	X-RAY DIFFRACTION	12	ALL	DDD	330 - 469

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+About Yorodumi

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Movie

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Structure viewers

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Viewer log

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This web site

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Open data

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Validation report

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Assembly

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

-
Non-polymers , 8 types, 1614 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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Feb 9, 2022. New format data for meta-information of EMDB entries

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

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Yorodumi