PDB-6f3m: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pse...

ID or keywords:

Entry

Database: PDB / ID: 6f3m

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa complexed with adenosine, K+ and Zn2+ cations

Components

(Adenosylhomocysteinase

) x 2

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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Czyrko, J. / Brzezinski, K.

Funding support

Poland, 1items

Citation

Journal: Sci Rep / Year: 2018
Title: Metal-cation regulation of enzyme dynamics is a key factor influencing the activity of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa.
Authors: Czyrko, J. / Sliwiak, J. / Imiolczyk, B. / Gdaniec, Z. / Jaskolski, M. / Brzezinski, K.

History

Deposition	Nov 28, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 8, 2018	Provider: repository / Type: Initial release
Revision 1.1	Jan 17, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6f3m.cif.gz	757 KB	Display	PDBx/mmCIF format
PDB format	pdb6f3m.ent.gz	619.1 KB	Display	PDB format
PDBx/mmJSON format	6f3m.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3m ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3m	HTTPS FTP

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Related structure data

Related structure data	6f3nC 6f3oC 6f3pSC 6f3qC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6f3q-d 6f3p-1 6f3o-d 6f3n-d 1k0u-1 5t8f-d 5axd-1 6pyr-d 1a7a-1 4pgf-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18430/M36F3M / Data set type: diffraction image data

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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

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration, light scattering

Unit cell

Length a, b, c (Å)	175.976, 104.145, 107.634
Angle α, β, γ (deg.)	90.00, 100.71, 90.00
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	C
1	3	A
2	3	D
1	4	B
2	4	C
1	5	B
2	5	D
1	6	C
2	6	D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / Refine code: 0

Dom-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	ARG	ARG	A	A	10 - 468	2 - 460
2	1	ARG	ARG	B	B	10 - 468	1 - 459
1	2	ARG	ARG	A	A	10 - 468	2 - 460
2	2	ARG	ARG	C	C	10 - 468	1 - 459
1	3	ARG	ARG	A	A	10 - 468	2 - 460
2	3	ARG	ARG	D	D	10 - 468	1 - 459
1	4	TYR	TYR	B	B	10 - 469	1 - 460
2	4	TYR	TYR	C	C	10 - 469	1 - 460
1	5	TYR	TYR	B	B	10 - 469	1 - 460
2	5	TYR	TYR	D	D	10 - 469	1 - 460
1	6	TYR	TYR	C	C	10 - 469	1 - 460
2	6	TYR	TYR	D	D	10 - 469	1 - 460

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 2 types, 4 molecules ABCD

#1: Protein	Adenosylhomocysteinase / / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 50673.809 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plusRIL / References: UniProt: Q9I685, adenosylhomocysteinase
#2: Protein	Adenosylhomocysteinase / / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 50616.758 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria) Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plusRIL / References: UniProt: Q9I685, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase /

/ S-adenosyl-L-homocysteine hydrolase / AdoHcyase

Mass: 50673.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plusRIL / References: UniProt: Q9I685,

adenosylhomocysteinase

#2: Protein

Adenosylhomocysteinase /

/ S-adenosyl-L-homocysteine hydrolase / AdoHcyase

Mass: 50616.758 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: ahcY, sahH, PA0432 / Plasmid: pMCSG57 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon plusRIL / References: UniProt: Q9I685,

adenosylhomocysteinase

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Non-polymers , 7 types, 1998 molecules

#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-ADN / ADENOSINE / Adenosine Mass: 267.241 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#7: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#8: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1975 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.39 Å³/Da / Density % sol: 48.59 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / Details: 50 mM KH2PO4, 20 % (W/V) PEG8000, 2 mM adenosine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 21, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.6→50 Å / Num. obs: 244909 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / R_merge(I) obs: 0.061 / Net I/σ(I): 14.9
Reflection shell	Resolution: 1.6→1.69 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6F3P

6f3p

Resolution: 1.6→48.7 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.959 / SU B: 3.011 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.074 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17421	2450	1 %	RANDOM
R_work	0.15097	-	-	-
obs	0.1512	242459	97.81 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 26.431 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.18 Å²	0 Å²	0.57 Å²
2-	-	0.03 Å²	-0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: 1 / Resolution: 1.6→48.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14196	0	298	1975	16469

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.019	14921
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14348
X-RAY DIFFRACTION	r_angle_refined_deg	1.58	1.953	20255
X-RAY DIFFRACTION	r_angle_other_deg	0.975	3	33086
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.421	5	1883
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.46	25.139	646
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.949	15	2624
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.793	15	71
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	2286
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	17447
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3248
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.808	1.681	7412
X-RAY DIFFRACTION	r_mcbond_other	0.808	1.681	7411
X-RAY DIFFRACTION	r_mcangle_it	1.134	2.522	9272
X-RAY DIFFRACTION	r_mcangle_other	1.134	2.522	9273
X-RAY DIFFRACTION	r_scbond_it	1.3	1.859	7509
X-RAY DIFFRACTION	r_scbond_other	1.3	1.856	7493
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	1.94	2.73	10939
X-RAY DIFFRACTION	r_long_range_B_refined	4.373	22.336	17726
X-RAY DIFFRACTION	r_long_range_B_other	4.096	21.175	17099
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	30680	0.06
1	2	B	30680	0.06
2	1	A	30840	0.05
2	2	C	30840	0.05
3	1	A	30950	0.06
3	2	D	30950	0.06
4	1	B	30884	0.06
4	2	C	30884	0.06
5	1	B	30836	0.07
5	2	D	30836	0.07
6	1	C	31180	0.05
6	2	D	31180	0.05

LS refinement shell

Resolution: 1.6→1.642 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	153	-
R_work	0.232	15084	-
obs	-	-	82.71 %

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	0.8575	0.108	-0.1671	0.4918	-0.1136	1.192	0.0226	0.0365	0.0944	-0.0248	-0.0078	-0.1231	-0.0199	0.2604	-0.0149	0.017	0.0107	0.0366	0.1371	0.0048	0.104	74.4902	27.1172	19.6375
2	0.6941	-0.1231	0.4102	0.5183	-0.0278	1.265	-0.0193	-0.0011	0.2198	-0.0091	-0.021	-0.1024	-0.2077	0.1025	0.0403	0.0413	-0.0186	0.0215	0.026	0.0022	0.1192	52.8987	43.7391	30.2049
3	0.8921	0.2718	0.1028	0.3078	-0.0254	0.4761	-0.0154	0.2091	0.0099	-0.1384	0.0235	-0.0816	0.0971	0.1334	-0.0082	0.0902	0.0367	0.0502	0.0993	0.0126	0.055	61.249	18.6543	6.186
4	0.8154	-0.1259	-0.2921	0.7019	0.1182	0.8865	0.0912	0.2259	0.0173	-0.3582	-0.0919	0.0277	-0.0078	-0.1275	0.0007	0.2343	0.0494	-0.0243	0.1348	0.0367	0.0328	27.1984	31.4179	-7.5026
5	1.3065	-0.2112	-0.1854	0.6436	0.0475	0.407	0.0028	0.1566	-0.1583	-0.1405	-0.0471	0.0639	0.1003	-0.0568	0.0444	0.0735	0.0019	-0.0045	0.0323	-0.022	0.0229	31.3872	9.8441	11.8741
6	0.6226	-0.049	0.2387	0.4413	0.0841	0.869	0.0132	0.1825	0.1271	-0.2892	-0.0263	-0.1811	-0.1375	0.1343	0.0131	0.2132	0.0106	0.101	0.0863	0.0588	0.1219	44.212	40.683	-0.139
7	0.8572	-0.1396	-0.1434	0.9623	-0.1533	0.947	-0.0488	-0.1822	0.0066	0.2385	0.0502	-0.1393	0.0137	0.1115	-0.0014	0.0637	0.0239	-0.0398	0.0799	-0.0266	0.0356	48.9276	27.8703	62.036
8	1.5684	0.1956	-0.1302	0.7593	0.1237	0.5781	-0.0177	-0.0608	-0.1259	-0.0024	0.0031	-0.1074	0.1218	0.0906	0.0145	0.027	0.0193	0.0062	0.0154	0.0069	0.0224	48.3494	9.1822	39.0528
9	0.6212	-0.203	-0.009	0.7579	0.0135	0.6154	-0.0509	-0.1264	0.0123	0.1456	0.0374	0.0119	-0.001	-0.0115	0.0134	0.0296	0.007	0.0028	0.0321	-0.0054	0.0024	36.7183	28.4669	53.2963
10	0.926	-0.0233	-0.3745	0.3138	-0.1239	1.0103	-0.0231	0.0343	-0.0354	-0.0201	0.0082	0.1183	0.0322	-0.1529	0.0149	0.0088	-0.0115	-0.0134	0.0386	-0.0065	0.071	3.8963	16.2881	33.8704
11	0.7722	-0.0302	0.4009	0.6533	0.0492	1.5739	-0.0148	0.0367	0.1466	-0.0932	-0.021	0.0988	-0.1803	-0.1236	0.0357	0.0334	0.0189	-0.0115	0.0183	0.007	0.0496	20.0289	40.2413	27.0464
12	0.8137	-0.2678	0.1446	0.2907	0.0235	0.1679	-0.0376	-0.1294	-0.1198	0.0584	0.0209	0.0954	0.0655	-0.0455	0.0167	0.0415	-0.0046	0.0211	0.0257	0.0073	0.0497	18.9236	10.4203	44.6228

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 204
2	X-RAY DIFFRACTION	2	A	205 - 381
3	X-RAY DIFFRACTION	3	A	382 - 469
4	X-RAY DIFFRACTION	4	B	10 - 201
5	X-RAY DIFFRACTION	5	B	202 - 381
6	X-RAY DIFFRACTION	6	B	382 - 469
7	X-RAY DIFFRACTION	7	C	10 - 205
8	X-RAY DIFFRACTION	8	C	206 - 353
9	X-RAY DIFFRACTION	9	C	354 - 469
10	X-RAY DIFFRACTION	10	D	10 - 206
11	X-RAY DIFFRACTION	11	D	207 - 373
12	X-RAY DIFFRACTION	12	D	374 - 469

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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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Movie

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Structure viewers

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This page

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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 , 2 types, 4 molecules ABCD

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Non-polymers , 7 types, 1998 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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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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Aug 12, 2020. Covid-19 info

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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