PDB-8ajs: Crystal structure of the F324A mutant of S-adenosyl-L-homocystein...

ID or keywords:

Entry

Database: PDB / ID: 8ajs

Title

Crystal structure of the F324A 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

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: 1.68 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 F324A 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	8ajs.cif.gz	711.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8ajs.ent.gz		Display	PDB format
PDBx/mmJSON format	8ajs.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ajs_validation.pdf.gz	5.3 MB	Display	wwPDB validaton report
Full document	8ajs_full_validation.pdf.gz	5.3 MB	Display
Data in XML	8ajs_validation.xml.gz	82 KB	Display
Data in CIF	8ajs_validation.cif.gz	122.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/8ajs ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8ajs	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

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

1

Idetical with deposited unit
defined by author
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	177.844, 134.962, 109.393
Angle α, β, γ (deg.)	90.000, 106.043, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	BBB-504- 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: 51658.938 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) / References: UniProt: Q9I685, adenosylhomocysteinase

#1: Protein

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

Mass: 51658.938 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) / References: UniProt: Q9I685, adenosylhomocysteinase

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Non-polymers , 6 types, 1703 molecules

#2: Chemical	ChemComp-NAD / 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
#3: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1689 / 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: 3.05 Å³/Da / Density % sol: 59.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop 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: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97625 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 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: 1.68→105.921 Å / Num. obs: 280732 / % possible obs: 99.6 % / Redundancy: 5.319 % / CC_1/2: 0.998 / R_merge(I) obs: 0.064 / Net I/σ(I): 11.76
Reflection shell	Resolution: 1.68→1.78 Å / Mean I/σ(I) obs: 1.02 / Num. unique obs: 44792 / CC_1/2: 0.56 / % possible all: 98.5

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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: 1.68→105.921 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.96 / SU B: 4.685 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.072 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.1778	1039	0.37 %
R_work	0.1509	279688	-
all	0.151	-	-
obs	-	280727	99.656 %

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: 39.342 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.701 Å²	0 Å²	-0.384 Å²
2-	-	-0.403 Å²	-0 Å²
3-	-	-	1.137 Å²

Refinement step

Cycle: LAST / Resolution: 1.68→105.921 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14184	0	264	1689	16137

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	14804
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14133
X-RAY DIFFRACTION	r_angle_refined_deg	1.382	1.638	20093
X-RAY DIFFRACTION	r_angle_other_deg	1.399	1.585	32596
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.456	5	1872
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.523	23.779	696
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.459	15	2582
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.92	15	67
X-RAY DIFFRACTION	r_chiral_restr	0.076	0.2	1979
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	16872
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	3166
X-RAY DIFFRACTION	r_nbd_refined	0.221	0.2	3145
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	13713
X-RAY DIFFRACTION	r_nbtor_refined	0.165	0.2	7316
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	6478
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.158	0.2	1420
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.238	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.074	0.2	13
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.076	0.2	6
X-RAY DIFFRACTION	r_nbd_other	0.135	0.2	37
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.157	0.2	21
X-RAY DIFFRACTION	r_mcbond_it	1.606	2.309	7430
X-RAY DIFFRACTION	r_mcbond_other	1.606	2.309	7429
X-RAY DIFFRACTION	r_mcangle_it	2.09	3.453	9299
X-RAY DIFFRACTION	r_mcangle_other	2.09	3.453	9300
X-RAY DIFFRACTION	r_scbond_it	2.789	2.63	7374
X-RAY DIFFRACTION	r_scbond_other	2.789	2.63	7374
X-RAY DIFFRACTION	r_scangle_it	4.066	3.834	10787
X-RAY DIFFRACTION	r_scangle_other	4.066	3.834	10788
X-RAY DIFFRACTION	r_lrange_it	5.799	47.456	67764
X-RAY DIFFRACTION	r_lrange_other	5.586	46.198	65834
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.058	0.05	15460
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.058	0.05	15466
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.063	0.05	15380
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.058	0.05	15324
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.059	0.05	15326
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.063	0.05	15379

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	0.05824	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.05824	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.05784	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.05784	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.06292	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.06292	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.05772	0.05009
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.05772	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.05917	0.05009
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.05917	0.05009
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.06253	0.05009
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.06253	0.05009

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 (%)
1.68-1.723	0.361	75	0.468	20177	X-RAY DIFFRACTION	97.2485
1.723-1.77	0.431	74	0.41	20123	X-RAY DIFFRACTION	99.63
1.77-1.821	0.313	73	0.361	19542	X-RAY DIFFRACTION	99.7255
1.821-1.877	0.319	71	0.297	18993	X-RAY DIFFRACTION	99.7749
1.877-1.939	0.265	68	0.24	18461	X-RAY DIFFRACTION	99.8706
1.939-2.007	0.219	67	0.197	17880	X-RAY DIFFRACTION	99.9276
2.007-2.083	0.203	64	0.17	17250	X-RAY DIFFRACTION	99.9365
2.083-2.168	0.182	61	0.147	16597	X-RAY DIFFRACTION	99.904
2.168-2.264	0.149	59	0.136	15922	X-RAY DIFFRACTION	99.9437
2.264-2.374	0.154	57	0.123	15262	X-RAY DIFFRACTION	99.8696
2.374-2.503	0.165	54	0.121	14464	X-RAY DIFFRACTION	99.9449
2.503-2.655	0.131	51	0.116	13735	X-RAY DIFFRACTION	99.9492
2.655-2.838	0.139	48	0.12	12859	X-RAY DIFFRACTION	99.9768
2.838-3.065	0.197	44	0.14	12026	X-RAY DIFFRACTION	99.942
3.065-3.357	0.164	41	0.148	11057	X-RAY DIFFRACTION	99.964
3.357-3.753	0.175	37	0.138	10003	X-RAY DIFFRACTION	99.8707
3.753-4.333	0.127	33	0.119	8814	X-RAY DIFFRACTION	99.7407
4.333-5.304	0.145	28	0.108	7491	X-RAY DIFFRACTION	99.7612
5.304-7.492	0.124	22	0.162	5814	X-RAY DIFFRACTION	99.9657
7.492-105.921	0.345	12	0.183	3218	X-RAY DIFFRACTION	98.626

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	2.3251	0.1461	-0.4568	1.1622	0.0526	0.8363	0.0355	0.008	0.3814	-0.0598	0.053	-0.1576	-0.2255	0.122	-0.0885	0.155	-0.1042	-0.0277	0.0905	-0.0197	0.222	49.0125	34.1927	35.1191
2	1.1998	-0.0835	0.0639	0.9654	0.5091	0.819	0.0124	0.2495	0.1479	-0.2737	0.0379	-0.0945	-0.175	0.0735	-0.0503	0.1678	-0.0775	-0.028	0.1184	0.0589	0.0652	37.4071	17.7312	15.3468
3	0.7309	0.2989	-0.2111	1.0888	0.1802	0.802	0.0231	0.0381	0.0863	-0.1128	0.056	-0.2265	-0.1366	0.1421	-0.0791	0.1085	-0.081	0.0034	0.0867	0.0068	0.1052	45.9486	19.367	28.3564
4	1.6224	0.2678	-0.1792	1.7522	0.1792	1.3636	-0.0337	-0.0625	0.3725	0.079	-0.0316	0.448	-0.2853	-0.3451	0.0653	0.186	0.0778	-0.0917	0.1762	0.0016	0.3436	1.0089	30.793	30.9627
5	1.3524	0.2017	0.3205	1.905	0.0002	1.018	0.0396	-0.0963	0.1122	0.1422	-0.0199	0.2033	-0.0102	-0.1458	-0.0197	0.0661	-0.0291	-0.02	0.0629	0.0015	0.0639	16.0787	9.9979	42.423
6	0.7255	0.37	0.6989	1.0181	0.7791	1.7236	-0.0151	-0.0757	0.2312	-0.0366	-0.0903	0.3039	-0.086	-0.3354	0.1053	0.0776	-0.0058	-0.0402	0.119	0.0324	0.1968	6.9009	15.8764	31.582
7	2.3474	0.038	0.0608	1.1461	0.3032	0.7927	0.0153	0.0545	-0.2921	-0.044	-0.0163	0.2109	0.1771	-0.125	0.001	0.1218	-0.0863	-0.074	0.0717	0.0277	0.1356	6.97	-29.5584	28.444
8	0.7599	-0.0934	0.1017	1.1153	-0.441	0.8137	0.0099	0.1761	-0.0032	-0.111	-0.003	0.1253	0.0152	-0.0257	-0.0069	0.1162	-0.0477	-0.0847	0.1129	0.0217	0.0669	14.3588	-6.2018	13.9555
9	0.759	0.3066	0.2389	1.2174	-0.0873	0.4519	0.0235	0.0277	-0.0092	-0.0134	0.0078	0.2621	0.1109	-0.1042	-0.0313	0.0952	-0.0672	-0.0607	0.0612	0.0251	0.1195	9.1719	-13.6819	26.8142
10	1.9585	0.2602	0.1853	2.2891	-0.1824	1.0344	-0.022	0.2571	-0.251	-0.1788	0.0622	-0.5087	0.2111	0.3435	-0.0402	0.185	0.0223	0.0399	0.2474	-0.1084	0.2142	52.2222	-22.4795	12.456
11	1.1928	0.3814	-0.0888	1.7412	0.2222	1.2588	0.0183	-0.0412	-0.0911	0.0713	0.0401	-0.2591	0.0069	0.1632	-0.0584	0.0596	-0.0262	-0.0584	0.059	0.0107	0.0814	42.0946	-8.4275	34.906
12	0.8593	0.3216	-0.2502	1.578	-0.6879	1.2886	-0.0363	0.1144	-0.1286	-0.1641	-0.0173	-0.4066	0.0116	0.2891	0.0536	0.0917	-0.0324	0.001	0.1412	-0.0351	0.1589	47.705	-9.2533	20.5507

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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Protein , 1 types, 4 molecules AAABBBCCCDDD

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Non-polymers , 6 types, 1703 molecules

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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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-Protein , 1 types, 4 molecules AAABBBCCCDDD

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Assembly

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Protein , 1 types, 4 molecules AAABBBCCCDDD

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Non-polymers , 6 types, 1703 molecules

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Details

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Experimental details

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Experiment

-
Sample preparation

-
Data collection

-
Processing

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About Yorodumi

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News

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

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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

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Jul 12, 2017. Major update of PDB

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