PDB-6f3o: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pse...

ID or keywords:

Entry

Database: PDB / ID: 6f3o

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Pseudomonas aeruginosa complexed with adenine, K+ and Zn2+ 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 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.75 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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_label_asym_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_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	6f3o.cif.gz	730.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6f3o.ent.gz	602.4 KB	Display	PDB format
PDBx/mmJSON format	6f3o.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3o ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3o	HTTPS FTP

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Related structure data

Related structure data	6f3mC 6f3nC 6f3pSC 6f3qC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6f3m-d 6f3q-d 6f3p-1 1a7a-1 1li4-1 3nj4-d 2h5l-1 1d4f-d 1k0u-1 5axb-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/M36F3O / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#210 - Jun 2017 Adenine Riboswitch in Action similarity (1) #130 - Oct 2010 Riboswitches similarity (1) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1)

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: 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&software
Evidence: gel filtration, light scattering

Unit cell

Length a, b, c (Å)	170.839, 99.614, 111.825
Angle α, β, γ (deg.)	90.00, 101.97, 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	TYR	TYR	A	A	10 - 469	13 - 472
2	1	TYR	TYR	B	B	10 - 469	13 - 472
1	2	TYR	TYR	A	A	10 - 469	13 - 472
2	2	TYR	TYR	C	C	10 - 469	13 - 472
1	3	ARG	ARG	A	A	10 - 468	13 - 471
2	3	ARG	ARG	D	D	10 - 468	13 - 471
1	4	TYR	TYR	B	B	10 - 469	13 - 472
2	4	TYR	TYR	C	C	10 - 469	13 - 472
1	5	ARG	ARG	B	B	10 - 468	13 - 471
2	5	ARG	ARG	D	D	10 - 468	13 - 471
1	6	ARG	ARG	C	C	10 - 468	13 - 471
2	6	ARG	ARG	D	D	10 - 468	13 - 471

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Adenosylhomocysteinase / / S-adenosyl-L-homocysteine hydrolase / AdoHcyase Mass: 51735.031 Da / Num. of mol.: 4 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): CodonPlus RILP / References: UniProt: Q9I685, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase /

/ S-adenosyl-L-homocysteine hydrolase / AdoHcyase

Mass: 51735.031 Da / Num. of mol.: 4
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): CodonPlus RILP / References: UniProt: Q9I685,

adenosylhomocysteinase

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Non-polymers , 7 types, 1639 molecules

#2: Chemical	ChemComp-K / POTASSIUM ION Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#3: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO₄
#4: 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
#5: Chemical	ChemComp-ADE / ADENINE / Adenine Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₅H₅N₅
#6: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1616 / 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: 2.25 Å³/Da / Density % sol: 45.31 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 50 mM KH2PO4, 20% (w/v) PEG8000, 2 mM 2'-deoxyadenosine

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.895 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 6, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.895 Å / Relative weight: 1
Reflection	Resolution: 1.75→25 Å / Num. obs: 182928 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / R_merge(I) obs: 0.078 / Net I/σ(I): 17.6
Reflection shell	Resolution: 1.75→1.81 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing
ARP/wARP		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6F3P

6f3p

Resolution: 1.75→25 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.953 / SU B: 3.123 / SU ML: 0.054 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.088 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.16712	1806	1 %	RANDOM
R_work	0.13976	-	-	-
obs	0.14003	181035	99.69 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 25.543 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.03 Å²	-0 Å²	-0.08 Å²
2-	-	0.24 Å²	0 Å²
3-	-	-	-0.22 Å²

Refinement step

Cycle: 1 / Resolution: 1.75→25 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14196	0	268	1616	16080

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	14981
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14411
X-RAY DIFFRACTION	r_angle_refined_deg	1.657	1.955	20356
X-RAY DIFFRACTION	r_angle_other_deg	0.983	3	33226
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.351	5	1915
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.562	25.184	652
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.988	15	2648
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.423	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	2284
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	17627
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3285
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	1.052	1.849	7459
X-RAY DIFFRACTION	r_mcbond_other	1.052	1.849	7458
X-RAY DIFFRACTION	r_mcangle_it	1.494	2.771	9345
X-RAY DIFFRACTION	r_mcangle_other	1.494	2.771	9346
X-RAY DIFFRACTION	r_scbond_it	1.631	2.068	7522
X-RAY DIFFRACTION	r_scbond_other	1.631	2.068	7522
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.501	3.03	10980
X-RAY DIFFRACTION	r_long_range_B_refined	4.235	23.674	17424
X-RAY DIFFRACTION	r_long_range_B_other	4.066	22.97	17011
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	30682	0.07
1	2	B	30682	0.07
2	1	A	30784	0.07
2	2	C	30784	0.07
3	1	A	30922	0.06
3	2	D	30922	0.06
4	1	B	30556	0.06
4	2	C	30556	0.06
5	1	B	30618	0.06
5	2	D	30618	0.06
6	1	C	30734	0.06
6	2	D	30734	0.06

LS refinement shell

Resolution: 1.753→1.798 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.196	133	-
R_work	0.177	13008	-
obs	-	-	97.39 %

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	0.24	0.0344	-0.1548	0.1715	-0.0235	0.4893	-0.0236	0.0036	0.0015	0.0345	-0.0134	-0.017	-0.0044	0.0954	0.037	0.012	-0.0067	-0.0087	0.066	0.0184	0.076	72.3246	16.1897	19.3771
2	0.0405	-0.0683	0.1026	0.2402	-0.0591	0.424	-0.0072	0.0054	0.0016	0.04	-0.001	-0.0279	-0.0515	0.0209	0.0081	0.0656	-0.0203	-0.0129	0.0213	0.0087	0.0775	54.2177	37.3781	27.8641
3	0.4866	0.0633	-0.0811	0.0416	-0.0186	0.028	0.0124	0.0359	-0.0149	-0.0068	-0.0225	-0.0122	0.0224	0.014	0.0101	0.0516	0.0232	0.0132	0.0475	0.0086	0.0784	57.4392	8.3481	7.175
4	0.104	0.0587	-0.0763	0.1195	0.0609	0.3903	0.0078	0.003	-0.0098	-0.0215	-0.0144	-0.0075	-0.0249	-0.0311	0.0065	0.048	0.0071	0.0062	0.0334	0.0005	0.0647	24.9101	24.7478	-8.632
5	0.481	-0.0255	-0.0951	0.1645	0.0001	0.0644	-0.033	0.0193	-0.0572	0.0196	-0.003	0.0085	-0.0102	0.0018	0.0361	0.0435	-0.0023	0.0189	0.0261	-0.0059	0.0791	27.2905	6.0974	13.8156
6	0.098	0.0551	0.1764	0.0932	0.0466	0.3655	-0.014	0.0106	0.0061	-0.0245	-0.0152	-0.0246	-0.0173	0.0298	0.0292	0.0556	-0.0017	0.021	0.0366	0.0084	0.0747	44.067	31.8854	-1.8828
7	0.2146	-0.3011	-0.2715	0.5422	0.3496	0.4122	-0.1343	-0.0334	0.0442	0.2572	0.1383	-0.0564	0.1071	0.0269	-0.004	0.1958	0.05	-0.0721	0.0566	0.0001	0.0358	48.4446	26.6139	61.4907
8	0.4195	0.0515	-0.0685	0.2189	0.0285	0.1185	-0.0565	-0.0167	-0.0194	0.0378	0.0084	-0.015	0.0177	0.0031	0.0481	0.0719	0.007	0.01	0.0227	0.0176	0.0541	46.1088	5.5543	41.5515
9	0.1544	-0.2066	0.1686	0.4299	-0.0076	0.4958	-0.0874	-0.0198	0.0287	0.1631	0.0153	-0.0103	-0.0201	-0.0369	0.0721	0.1264	0.0081	0.0078	0.0066	-0.0143	0.0456	30.4055	34.7116	55.3176
10	0.2507	-0.0963	0.0105	0.0456	0.0057	0.28	-0.0204	-0.0097	-0.0055	0.0002	-0.0153	-0.0074	-0.0004	-0.0581	0.0358	0.0326	-0.0066	0.0224	0.0649	-0.0096	0.0567	1.1567	18.8132	35.1661
11	0.0516	-0.0123	0.157	0.2454	0.0458	0.6254	-0.0043	-0.0104	-0.0098	-0.0058	-0.0187	-0.0069	-0.0869	-0.047	0.0231	0.0734	0.0125	0.007	0.0255	-0.009	0.0637	20.6242	38.3594	25.2553
12	0.5031	-0.1134	-0.0803	0.0269	0.0191	0.0231	-0.0147	-0.0369	-0.0088	0.0045	0.0046	-0.0046	0.0226	-0.0146	0.0101	0.0791	-0.0151	0.0287	0.0604	-0.0008	0.0547	15.4578	11.2146	48.2088

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	10 - 205
2	X-RAY DIFFRACTION	2	A	206 - 381
3	X-RAY DIFFRACTION	3	A	382 - 469
4	X-RAY DIFFRACTION	4	B	10 - 194
5	X-RAY DIFFRACTION	5	B	195 - 381
6	X-RAY DIFFRACTION	6	B	382 - 469
7	X-RAY DIFFRACTION	7	C	10 - 205
8	X-RAY DIFFRACTION	8	C	206 - 381
9	X-RAY DIFFRACTION	9	C	382 - 469
10	X-RAY DIFFRACTION	10	D	9 - 205
11	X-RAY DIFFRACTION	11	D	206 - 381
12	X-RAY DIFFRACTION	12	D	382 - 469

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Protein , 1 types, 4 molecules ABCD

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