PDB-8ajw: Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine...

ID or keywords:

Entry

Database: PDB / ID: 8ajw

Title

Crystal structure of the Q65N mutant of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa cocrystallized with adenosine in the presence of K+ cations

Components

S-adenosyl-L-homocysteine hydrolase

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: 1.819 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 Q65N 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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PDBx/mmCIF format	8ajw.cif.gz	712.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8ajw.ent.gz		Display	PDB format
PDBx/mmJSON format	8ajw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ajw_validation.pdf.gz	2.9 MB	Display	wwPDB validaton report
Full document	8ajw_full_validation.pdf.gz	2.9 MB	Display
Data in XML	8ajw_validation.xml.gz	79.2 KB	Display
Data in CIF	8ajw_validation.cif.gz	115.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/8ajw ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8ajw	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: S-adenosyl-L-homocysteine hydrolase

BBB: S-adenosyl-L-homocysteine hydrolase

CCC: S-adenosyl-L-homocysteine hydrolase

DDD: S-adenosyl-L-homocysteine hydrolase

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)	74.503, 133.618, 100.865
Angle α, β, γ (deg.)	90.000, 103.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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

Dom-ID	Component-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	ARG	ARG	AAA	A	9 - 468	12 - 471
2	2	1	ARG	ARG	BBB	B	9 - 468	12 - 471
3	3	2	TYR	TYR	AAA	A	9 - 469	12 - 472
4	4	2	TYR	TYR	CCC	C	9 - 469	12 - 472
5	5	3	TYR	TYR	AAA	A	9 - 469	12 - 472
6	6	3	TYR	TYR	DDD	D	9 - 469	12 - 472
7	7	4	ARG	ARG	BBB	B	9 - 468	12 - 471
8	8	4	ARG	ARG	CCC	C	9 - 468	12 - 471
9	9	5	ARG	ARG	BBB	B	9 - 468	12 - 471
10	10	5	ARG	ARG	DDD	D	9 - 468	12 - 471
11	11	6	TYR	TYR	CCC	C	9 - 469	12 - 472
12	12	6	TYR	TYR	DDD	D	9 - 469	12 - 472

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	S-adenosyl-L-homocysteine hydrolase Mass: 51721.008 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / Variant (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685

#1: Protein

S-adenosyl-L-homocysteine hydrolase

Mass: 51721.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa PAO1 (bacteria) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus RILP / Variant (production host): BL21 CodonPlus RILP / References: UniProt: Q9I685

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Non-polymers , 5 types, 1337 molecules

#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / 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-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1324 / 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: 2.41 Å³/Da / Density % sol: 48.94 %
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: 0.9762 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: 0.9762 Å / Relative weight: 1
Reflection	Resolution: 1.819→79.133 Å / Num. obs: 171257 / % possible obs: 99.7 % / Redundancy: 6.87 % / CC_1/2: 0.999 / R_merge(I) obs: 0.097 / Net I/σ(I): 12.05
Reflection shell	Resolution: 1.819→1.917 Å / R_merge(I) obs: 0.144 / Mean I/σ(I) obs: 1.11 / Num. unique obs: 27398 / CC_1/2: 0.683 / R_rim(I) all: 0.156

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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: 1.819→79.133 Å / Cor.coef. F_o:F_c: 0.977 / Cor.coef. F_o:F_c free: 0.955 / SU B: 6.715 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.109 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.1941	1285	0.75 %
R_work	0.1596	169958	-
all	0.16	-	-
obs	-	171243	99.703 %

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: 36.188 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.157 Å²	-0 Å²	-2.189 Å²
2-	-	2.397 Å²	0 Å²
3-	-	-	-0.193 Å²

Refinement step

Cycle: LAST / Resolution: 1.819→79.133 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14224	0	279	1324	15827

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	15102
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	14378
X-RAY DIFFRACTION	r_angle_refined_deg	1.378	1.638	20528
X-RAY DIFFRACTION	r_angle_other_deg	1.35	1.585	33186
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.558	5	1926
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.748	23.684	722
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.355	15	2639
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.589	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.078	0.2	2015
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	17289
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3264
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	3332
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.184	0.2	14073
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	7418
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.08	0.2	6817
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	1267
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.118	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.291	0.2	17
X-RAY DIFFRACTION	r_nbd_other	0.317	0.2	80
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.171	0.2	20
X-RAY DIFFRACTION	r_mcbond_it	1.326	1.761	7551
X-RAY DIFFRACTION	r_mcbond_other	1.326	1.761	7550
X-RAY DIFFRACTION	r_mcangle_it	1.872	2.636	9474
X-RAY DIFFRACTION	r_mcangle_other	1.872	2.636	9475
X-RAY DIFFRACTION	r_scbond_it	1.919	1.99	7551
X-RAY DIFFRACTION	r_scbond_other	1.894	1.984	7535
X-RAY DIFFRACTION	r_scangle_it	2.811	2.916	11036
X-RAY DIFFRACTION	r_scangle_other	2.783	2.908	11013
X-RAY DIFFRACTION	r_lrange_it	4.908	35.27	67227
X-RAY DIFFRACTION	r_lrange_other	4.771	34.449	65984
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.066	0.05	15611
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.066	0.05	15659
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.067	0.05	15640
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.066	0.05	15488
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.067	0.05	15452
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.067	0.05	15505

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	0.06567	0.05009
1	2	BBB	X-RAY DIFFRACTION	Local ncs	0.06567	0.05009
2	3	AAA	X-RAY DIFFRACTION	Local ncs	0.06562	0.05009
2	4	CCC	X-RAY DIFFRACTION	Local ncs	0.06562	0.05009
3	5	AAA	X-RAY DIFFRACTION	Local ncs	0.06696	0.05009
3	6	DDD	X-RAY DIFFRACTION	Local ncs	0.06696	0.05009
4	7	BBB	X-RAY DIFFRACTION	Local ncs	0.06572	0.05009
4	8	CCC	X-RAY DIFFRACTION	Local ncs	0.06572	0.05009
5	9	BBB	X-RAY DIFFRACTION	Local ncs	0.06712	0.05009
5	10	DDD	X-RAY DIFFRACTION	Local ncs	0.06712	0.05009
6	11	CCC	X-RAY DIFFRACTION	Local ncs	0.06739	0.05009
6	12	DDD	X-RAY DIFFRACTION	Local ncs	0.06739	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
1.819-1.866	0.331	94	0.359	12376	0.358	12654	0.484	0.452	98.5459	0.354
1.866-1.917	0.343	91	0.308	12138	0.309	12299	0.645	0.688	99.4308	0.295
1.917-1.973	0.293	90	0.269	11860	0.269	12007	0.794	0.8	99.5253	0.249
1.973-2.034	0.276	87	0.243	11528	0.243	11661	0.847	0.848	99.6055	0.22
2.034-2.1	0.273	85	0.215	11224	0.216	11344	0.869	0.89	99.6915	0.191
2.1-2.174	0.22	82	0.191	10821	0.191	10935	0.9	0.918	99.7074	0.166
2.174-2.256	0.22	79	0.166	10486	0.167	10587	0.93	0.945	99.7922	0.142
2.256-2.348	0.152	76	0.145	10072	0.145	10175	0.96	0.96	99.7346	0.123
2.348-2.452	0.172	73	0.139	9635	0.139	9717	0.962	0.966	99.9074	0.118
2.452-2.572	0.171	70	0.136	9274	0.137	9346	0.962	0.969	99.9786	0.117
2.572-2.711	0.202	66	0.142	8796	0.143	8864	0.951	0.966	99.9774	0.124
2.711-2.875	0.176	63	0.143	8326	0.144	8389	0.95	0.964	100	0.13
2.875-3.073	0.214	60	0.152	7836	0.153	7896	0.941	0.96	100	0.141
3.073-3.319	0.214	55	0.154	7289	0.155	7344	0.954	0.963	100	0.147
3.319-3.635	0.163	51	0.146	6739	0.146	6790	0.968	0.974	100	0.145
3.635-4.063	0.151	46	0.133	6089	0.133	6137	0.971	0.979	99.9674	0.138
4.063-4.69	0.101	40	0.11	5377	0.11	5420	0.985	0.984	99.9446	0.124
4.69-5.739	0.182	35	0.135	4570	0.136	4605	0.972	0.978	100	0.155
5.739-8.095	0.2	26	0.17	3534	0.171	3560	0.942	0.954	100	0.194
8.095-79.133	0.295	16	0.181	1989	0.182	2023	0.852	0.941	99.1102	0.226

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	1.525	-0.474	0.2417	1.5348	0.1755	1.3917	-0.121	-0.2767	0.0566	0.3071	0.1565	-0.0607	-0.0088	-0.0345	-0.0355	0.2408	0.0665	-0.0645	0.0848	-0.037	0.1213	10.562	4.7727	13.5
2	0.9254	-0.3998	-0.0014	1.0363	0.0129	0.9264	-0.0063	0.0072	0.1586	-0.0547	0.0417	-0.2366	-0.0827	0.1636	-0.0354	0.1378	-0.0207	-0.024	0.035	-0.0337	0.1904	19.9451	7.4412	-12.9647
3	0.6573	-0.2592	0.0898	1.1525	0.1088	0.6958	-0.0415	-0.1081	0.0283	0.1491	0.0784	-0.1484	0.0087	0.0946	-0.0369	0.1305	0.0149	-0.0531	0.0481	-0.0267	0.1204	14.547	-0.8462	-1.5146
4	1.5812	-0.3136	-0.0486	1.7856	0.4197	1.9071	-0.0317	0.0805	0.116	-0.2416	-0.1082	0.2447	-0.2135	-0.2207	0.1399	0.2777	0.0651	-0.1258	0.0405	-0.0547	0.2264	-14.3478	30.4331	-19.2652
5	0.989	-0.0526	0.5739	1.3336	0.1785	1.3129	-0.0138	-0.0283	-0.0638	-0.0959	-0.0549	0.2554	-0.114	-0.2096	0.0687	0.1369	0.0364	-0.061	0.0451	-0.0486	0.1836	-14.0363	2.0251	-19.6343
6	0.8299	-0.0901	-0.0216	1.0922	-0.1129	1.4275	-0.0475	0.0648	0.0537	-0.2427	-0.0441	0.1611	-0.2606	-0.2339	0.0916	0.2357	0.0508	-0.1111	0.0507	-0.0452	0.194	-10.8491	15.8892	-25.6933
7	1.2392	-0.527	0.6595	1.4041	-0.0515	1.8906	0.1366	0.283	-0.1224	-0.2976	-0.1129	0.0656	0.0121	0.0813	-0.0237	0.302	0.09	-0.1267	0.1564	-0.1228	0.1927	-7.5953	-15.8308	-57.9351
8	0.992	-0.2337	0.352	1.0564	0.2382	0.7704	0.053	0.2415	0.0839	-0.3355	-0.0418	-0.0755	-0.2149	0.1732	-0.0112	0.3134	-0.0084	-0.0099	0.1052	-0.0116	0.1546	7.9646	3.0388	-43.6613
9	0.2946	-0.2429	0.2335	0.7084	0.2279	1.0958	0.0706	0.1454	-0.0195	-0.2853	-0.09	0.0452	-0.143	0.0109	0.0193	0.2724	0.051	-0.0871	0.1145	-0.0535	0.1686	-4.9235	-4.7908	-46.449
10	1.7079	-0.0574	0.2708	1.3722	0.0301	1.6839	0.0955	0.1723	-0.3951	-0.055	0.0376	-0.2941	0.2989	0.3848	-0.1331	0.2412	0.1084	-0.0377	0.2495	-0.1863	0.4205	31.7792	-28.93	-32.6256
11	1.0067	-0.0865	0.2596	1.0859	0.2331	2.1185	0.0798	-0.0468	-0.2112	0.0234	0.0195	-0.0285	0.2456	0.0746	-0.0994	0.1658	0.0179	-0.0641	0.0124	-0.0224	0.1871	7.5296	-22.2697	-19.8665
12	1.0827	0.3062	0.2886	1.3027	0.5701	0.9729	0.0985	0.0161	-0.2634	0.0671	0.0744	-0.3047	0.2157	0.2287	-0.1729	0.1888	0.0594	-0.0468	0.0874	-0.0401	0.2179	22.5573	-20.1764	-22.95

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 , 5 types, 1337 molecules

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Experiment

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-Protein , 1 types, 4 molecules AAABBBCCCDDD

-Non-polymers , 5 types, 1337 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

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

-
Assembly

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

-
Non-polymers , 5 types, 1337 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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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Yorodumi