PDB-8aju: Crystal structure of the Q65A mutant of S-adenosyl-L-homocysteine...

ID or keywords:

Entry

Database: PDB / ID: 8aju

Title

Crystal structure of the Q65A 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: 1.645 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 Q65A 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	8aju.cif.gz	376.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8aju.ent.gz		Display	PDB format
PDBx/mmJSON format	8aju.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8aju_validation.pdf.gz	2.5 MB	Display	wwPDB validaton report
Full document	8aju_full_validation.pdf.gz	2.5 MB	Display
Data in XML	8aju_validation.xml.gz	47.8 KB	Display
Data in CIF	8aju_validation.cif.gz	73 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aj/8aju ftp://data.pdbj.org/pub/pdb/validation_reports/aj/8aju	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

CCC: Adenosylhomocysteinase

hetero molecules

105 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

AAA: Adenosylhomocysteinase

CCC: Adenosylhomocysteinase

hetero molecules

AAA: Adenosylhomocysteinase

CCC: Adenosylhomocysteinase

hetero molecules

defined by author&software
Evidence: gel filtration
211 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	142.132, 85.925, 125.568
Angle α, β, γ (deg.)	90.000, 131.184, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	AAA-1004- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	AAA
2	1	CCC

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 10 - 469 / Label seq-ID: 13 - 472

Dom-ID	Component-ID	Auth asym-ID	Label asym-ID
1	1	AAA	A
2	2	CCC	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Protein , 1 types, 2 molecules AAACCC

#1: Protein	Adenosylhomocysteinase / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 51677.984 Da / Num. of mol.: 2 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: 51677.984 Da / Num. of mol.: 2
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 , 5 types, 1126 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO₄ / Feature type: SUBJECT OF INVESTIGATION
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1119 / 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: 2.79 Å³/Da / Density % sol: 55.94 %
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: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 7, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.645→41.679 Å / Num. obs: 136460 / % possible obs: 98.8 % / Redundancy: 3.764 % / CC_1/2: 0.995 / Net I/σ(I): 7.57
Reflection shell	Resolution: 1.65→1.74 Å / Mean I/σ(I) obs: 1.14 / Num. unique obs: 21330 / CC_1/2: 0.543 / % possible all: 95.9

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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: 1.645→41.679 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.953 / SU B: 4.827 / SU ML: 0.081 / Cross valid method: FREE R-VALUE / ESU R: 0.08 / ESU R Free: 0.083 / Details: HYDROGEN ATOMS WERE ADDED AT RIDING POSITIONS

	R_factor	Num. reflection	% reflection
R_free	0.1983	2101	1.54 %
R_work	0.1665	134358	-
all	0.167	-	-
obs	-	136459	99.115 %

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: 30.907 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.635 Å²	0 Å²	0.034 Å²
2-	-	0.057 Å²	0 Å²
3-	-	-	0.205 Å²

Refinement step

Cycle: LAST / Resolution: 1.645→41.679 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7088	0	142	1119	8349

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.013	7526
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	7112
X-RAY DIFFRACTION	r_angle_refined_deg	1.629	1.636	10243
X-RAY DIFFRACTION	r_angle_other_deg	1.466	1.584	16390
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.358	5	977
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.264	23.683	353
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.082	15	1283
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.857	15	34
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	1008
X-RAY DIFFRACTION	r_gen_planes_refined	0.012	0.02	8658
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1629
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1642
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.181	0.2	6892
X-RAY DIFFRACTION	r_nbtor_refined	0.168	0.2	3636
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.082	0.2	3219
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.171	0.2	792
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.121	0.2	23
X-RAY DIFFRACTION	r_nbd_other	0.167	0.2	117
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.199	0.2	77
X-RAY DIFFRACTION	r_mcbond_it	1.482	2.275	3796
X-RAY DIFFRACTION	r_mcbond_other	1.482	2.276	3795
X-RAY DIFFRACTION	r_mcangle_it	1.926	3.414	4764
X-RAY DIFFRACTION	r_mcangle_other	1.926	3.414	4765
X-RAY DIFFRACTION	r_scbond_it	2.033	2.463	3730
X-RAY DIFFRACTION	r_scbond_other	2.033	2.464	3731
X-RAY DIFFRACTION	r_scangle_it	2.786	3.633	5463
X-RAY DIFFRACTION	r_scangle_other	2.786	3.634	5464
X-RAY DIFFRACTION	r_lrange_it	4.828	46.068	34723
X-RAY DIFFRACTION	r_lrange_other	4.235	44.688	33439
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.058	0.05	15448

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	0.05811	0.05009
1	2	CCC	X-RAY DIFFRACTION	Local ncs	0.05811	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
1.645-1.688	0.336	144	0.315	9202	0.315	10197	0.599	0.63	91.6544	0.318
1.688-1.734	0.319	151	0.29	9670	0.291	9836	0.715	0.761	99.8475	0.29
1.734-1.784	0.285	148	0.267	9417	0.267	9582	0.805	0.806	99.8226	0.262
1.784-1.839	0.252	143	0.248	9176	0.248	9344	0.837	0.844	99.7324	0.238
1.839-1.899	0.264	139	0.23	8897	0.23	9060	0.858	0.861	99.7351	0.214
1.899-1.966	0.224	134	0.205	8598	0.205	8749	0.916	0.906	99.8057	0.186
1.966-2.04	0.212	130	0.195	8289	0.195	8426	0.882	0.896	99.9169	0.174
2.04-2.123	0.229	125	0.185	8006	0.185	8148	0.876	0.907	99.7914	0.163
2.123-2.217	0.196	120	0.156	7674	0.157	7798	0.942	0.953	99.9487	0.135
2.217-2.325	0.171	115	0.144	7345	0.145	7481	0.958	0.959	99.7193	0.123
2.325-2.45	0.171	109	0.136	6986	0.137	7110	0.96	0.962	99.789	0.117
2.45-2.598	0.199	103	0.143	6602	0.144	6735	0.952	0.96	99.5546	0.125
2.598-2.777	0.166	97	0.136	6203	0.136	6325	0.963	0.966	99.6047	0.12
2.777-2.998	0.171	90	0.131	5767	0.132	5863	0.961	0.97	99.8977	0.12
2.998-3.283	0.188	84	0.142	5366	0.142	5458	0.955	0.965	99.8534	0.134
3.283-3.668	0.176	75	0.141	4809	0.142	4906	0.959	0.969	99.5516	0.14
3.668-4.23	0.161	67	0.139	4257	0.139	4359	0.966	0.972	99.1971	0.143
4.23-5.167	0.156	57	0.134	3631	0.134	3721	0.971	0.973	99.1131	0.142
5.167-7.252	0.224	44	0.181	2840	0.181	2885	0.952	0.95	99.9653	0.186
7.252-41.679	0.238	26	0.205	1623	0.206	1684	0.932	0.949	97.9216	0.231

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	1.4078	-0.1921	-0.1828	0.7099	-0.2401	1.5807	-0.0229	-0.3446	0.0652	0.0824	0.0222	-0.1104	-0.0208	0.1358	0.0007	0.0225	-0.0038	-0.0274	0.1166	-0.0146	0.0379	30.1336	84.4256	23.3862
2	1.2143	0.1637	-0.2299	0.5307	0.1776	0.802	-0.0099	-0.1685	-0.1776	0.059	-0.0085	-0.0413	0.0489	0.0486	0.0184	0.0098	0.0014	-0.0061	0.0322	0.0339	0.0443	10.9884	66.9129	12.6442
3	0.7562	0.0151	0.0012	0.4339	0.1441	0.3234	-0.0062	-0.2506	0.003	0.0973	-0.0084	-0.0296	0.0148	0.0106	0.0146	0.024	-0.0021	-0.0099	0.092	0.0051	0.0073	14.9705	79.9445	19.2416
4	1.6645	0.3152	0.1667	1.1258	-0.1225	1.4676	-0.0603	0.4977	-0.0464	-0.1862	0.0614	-0.1438	-0.0097	0.1799	-0.0011	0.037	-0.0075	0.0323	0.1843	-0.0203	0.062	29.7365	74.3794	-23.4981
5	1.5737	-0.0906	0.3852	0.789	0.1398	0.8413	-0.0272	0.2299	0.1616	-0.0907	0.0025	-0.0349	-0.0512	0.0568	0.0247	0.0145	-0.0101	-0.006	0.0421	0.0354	0.036	10.6345	91.4337	-12.2878
6	1.088	0.3567	0.201	0.8881	0.3787	0.3907	-0.0405	0.33	-0.0262	-0.1587	0.0485	-0.0535	-0.0471	0.0594	-0.008	0.0308	0	0.0094	0.1103	0.0021	0.0118	14.986	78.8597	-18.6908

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	AAA	10 - 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	CCC	10 - 172
5	X-RAY DIFFRACTION	5	ALL	CCC	173 - 329
6	X-RAY DIFFRACTION	6	ALL	CCC	330 - 469

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