PDB-4lvc: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bra...

ID or keywords:

Entry

Database: PDB / ID: 4lvc

Title

Crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine

Components

S-adenosyl-L-homocysteine hydrolase (SAHase)

Keywords

HYDROLASE / cellular methylation / SAH hydrolysis / NAD+ cofactor / atmospheric nitrogen fixation / rhizobium-legume symbiosis / NAD+ cofactor complex

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

Bradyrhizobium elkanii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.74 Å

Authors

Manszewski, T. / Singh, K. / Imiolczyk, B. / Jaskolski, M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: An enzyme captured in two conformational states: crystal structure of S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii.
Authors: Manszewski, T. / Singh, K. / Imiolczyk, B. / Jaskolski, M.

History

Deposition	Jul 26, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 30, 2014	Provider: repository / Type: Initial release
Revision 1.1	Dec 9, 2015	Group: Database references
Revision 1.2	Dec 16, 2015	Group: Database references
Revision 1.3	Sep 20, 2023	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 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4lvc.cif.gz	792.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4lvc.ent.gz	656.8 KB	Display	PDB format
PDBx/mmJSON format	4lvc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4lvc_validation.pdf.gz	2.4 MB	Display	wwPDB validaton report
Full document	4lvc_full_validation.pdf.gz	2.4 MB	Display
Data in XML	4lvc_validation.xml.gz	85.9 KB	Display
Data in CIF	4lvc_validation.cif.gz	127.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lv/4lvc ftp://data.pdbj.org/pub/pdb/validation_reports/lv/4lvc	HTTPS FTP

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Related structure data

Related structure data	3n58S 1b3r 1li4 3ond 3one 3onf S: Starting model for refinement
Similar structure data	2zj0-d 5m5k-d 3ond-1 1v8b-d 2ziz-d 3onf-1 3n58-d 3ce6-d 3one-1 2zj1-d Search similar-shape structures by Omokage search (details) 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) #135 - Mar 2011 Integrase similarity (1)

Deposited unit

A: S-adenosyl-L-homocysteine hydrolase (SAHase)

B: S-adenosyl-L-homocysteine hydrolase (SAHase)

C: S-adenosyl-L-homocysteine hydrolase (SAHase)

D: S-adenosyl-L-homocysteine hydrolase (SAHase)

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	107.720, 176.470, 104.270
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P2₁2₁2

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Protein , 1 types, 4 molecules ABCD

#1: Protein	S-adenosyl-L-homocysteine hydrolase (SAHase) Mass: 52737.238 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bradyrhizobium elkanii (bacteria) / Gene: BeSAHase / Plasmid: pET151/D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star References: UniProt: A0A087WNH6*PLUS, adenosylhomocysteinase

#1: Protein

S-adenosyl-L-homocysteine hydrolase (SAHase)

Mass: 52737.238 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bradyrhizobium elkanii (bacteria) / Gene: BeSAHase / Plasmid: pET151/D-TOPO / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21Star
References: UniProt: A0A087WNH6*PLUS, adenosylhomocysteinase

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Non-polymers , 6 types, 1732 molecules

#2: Chemical	ChemComp-ADN / ADENOSINE Mass: 267.241 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₄
#3: Chemical	ChemComp-NH4 / AMMONIUM ION Mass: 18.038 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: H₄N
#4: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1704 / 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: 2.35 Å³/Da / Density % sol: 47.64 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 0.2 M ammonium acetate, pH 7.1, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

BESSY

/ Beamline: 14.1 / Wavelength: 0.91841 Å

Detector

Type: RAYONIX MX-225 / Detector: CCD / Date: Apr 26, 2011 / Details: mirrors

Radiation

Monochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.91841 Å / Relative weight: 1

Reflection

Number: 1278402 / R_merge(I) obs: 0.086 / D res high: 1.74 Å / Num. obs: 200550 / % possible obs: 98.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	Num. obs	% possible obs (%)	ID	R_merge(I) obs
5.5	7.78	4321	99.8	1	0.065
4.49	5.5	5531	99.8	1	0.063
3.89	4.49	6486	99.8	1	0.066
3.48	3.89	7265	99.7	1	0.076
3.18	3.48	8035	99.6	1	0.086
2.94	3.18	8713	99.7	1	0.095
2.75	2.94	9316	99.7	1	0.083
2.59	2.75	9960	99.8	1	0.1
2.46	2.59	10450	99.8	1	0.114
2.35	2.46	10992	99.9	1	0.134
2.25	2.35	11534	99.9	1	0.157
2.16	2.25	11968	99.9	1	0.188
2.08	2.16	12449	99.9	1	0.228
2.01	2.08	12881	100	1	0.296
1.95	2.01	12852	96.3	1	0.282
1.89	1.95	13262	96.5	1	0.33
1.83	1.89	13603	96.4	1	0.428
1.79	1.83	14054	96.6	1	0.542
1.74	1.79	14401	97	1	0.694

Reflection

Resolution: 1.74→47.85 Å / Num. all: 203245 / Num. obs: 200550 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 6.37 % / R_merge(I) obs: 0.086 / Net I/σ(I): 12.34

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.74-1.79	0.694	1.95	1	97
1.79-1.83	0.542	2.49	1	96.6
1.83-1.89	0.428	3.09	1	96.4
1.89-1.95	0.33	3.92	1	96.5
1.95-2.01	0.282	4.91	1	96.3
2.01-2.08	0.296	6.64	1	100
2.08-2.16	0.228	8.29	1	99.9
2.16-2.25	0.188	9.81	1	99.9
2.25-2.35	0.157	11.44	1	99.9
2.35-2.46	0.134	13.09	1	99.9
2.46-2.59	0.114	15.04	1	99.8
2.59-2.75	0.1	16.84	1	99.8
2.75-2.94	0.083	19.49	1	99.7
2.94-3.18	0.095	22.14	1	99.7
3.18-3.48	0.086	25.44	1	99.6
3.48-3.89	0.076	28.12	1	99.7
3.89-4.49	0.066	29.99	1	99.8
4.49-5.5	0.063	30.63	1	99.8
5.5-7.78	0.065	29.26	1	99.8

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
REFMAC	5.5.0109	refinement
PDB_EXTRACT	3.11	data extraction
MxCuBE		data collection
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3N58

3n58

Resolution: 1.74→47.85 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.969 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.279 / SU ML: 0.063 / SU R Cruickshank DPI: 0.0925 / Cross valid method: R-FREE / ESU R: 0.091 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Hydrogen atoms were added at riding positions

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17222	1011	0.5 %	RANDOM
R_work	0.14763	-	-	-
obs	0.14775	199538	100 %	-
all	-	203245	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 21.592 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0 Å²
2-	-	-0.07 Å²	0 Å²
3-	-	-	0.06 Å²

Refinement step

Cycle: LAST / Resolution: 1.74→47.85 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14468	0	338	1704	16510

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	15275
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	10316
X-RAY DIFFRACTION	r_angle_refined_deg	1.618	1.982	20677
X-RAY DIFFRACTION	r_angle_other_deg	0.961	3	25207
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.02	5	1910
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.013	24.345	656
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.317	15	2643
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.545	15	87
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	2295
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	16925
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	3019
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	0.907	1.5	9384
X-RAY DIFFRACTION	r_mcbond_other	0.283	1.5	3878
X-RAY DIFFRACTION	r_mcangle_it	1.599	2	15052
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	2.568	3	5891
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	4.115	4.5	5618
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.74→1.785 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.243	72	-
R_work	0.24	14294	-
obs	-	-	100 %

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	0.1253	0.1924	0.1462	0.6139	0.1785	0.328	0.0029	-0.0345	0.0478	-0.0059	-0.0221	0.046	-0.0549	-0.0104	0.0193	0.075	-0.0064	0.0401	0.0259	-0.0361	0.0873	81.3672	86.5449	93.2297
2	0.2133	0.0857	-0.0816	0.3402	-0.0776	0.5817	0.0295	-0.0523	0.0295	-0.0203	0.0211	0.0063	-0.0506	0.0849	-0.0506	0.0428	-0.0337	0.0159	0.0667	-0.0248	0.06	98.3953	67.5266	81.3937
3	0.0758	0.2378	0.0172	0.966	0.0705	0.0133	0.0364	-0.0468	0.0534	0.087	-0.0339	0.1277	-0.0105	-0.0128	-0.0025	0.0525	-0.0101	0.0551	0.0985	-0.0349	0.0696	69.9279	64.5622	100.5685
4	0.5671	0.0725	-0.1287	0.1995	0.0326	0.5027	0.0343	-0.2416	-0.0667	0.0295	-0.0571	-0.0124	0.0522	0.0662	0.0229	0.0738	0.0002	-0.015	0.1466	0.0561	0.0354	84.8841	31.861	115.5554
5	0.3595	0.0413	-0.0333	0.3146	-0.0261	0.3451	0.0268	-0.0653	-0.0285	-0.0001	0.0063	0.0235	0.0368	-0.0352	-0.033	0.0447	-0.0113	0.0033	0.0672	0.0222	0.0634	72.2474	37.7688	91.753
6	0.2097	0.2269	-0.3869	0.3273	-0.4812	0.8958	0.0688	-0.171	-0.0011	0.107	-0.1122	-0.0175	-0.1086	0.2054	0.0434	0.0716	-0.0282	-0.0337	0.2302	-0.0428	0.0595	96.2229	54.657	107.9513
7	0.521	-0.0242	-0.0397	0.3891	0.088	0.3054	0.0065	0.1208	0.0723	-0.0637	0.0449	0.0303	-0.0385	0.0204	-0.0514	0.0844	-0.0371	0.004	0.065	0.0328	0.0388	87.712	66.7183	44.2512
8	0.239	0.0663	-0.0179	0.4705	0.0307	0.2505	-0.0092	0.0276	0.0561	-0.0274	0.043	0.037	-0.0018	-0.0252	-0.0338	0.0461	-0.0078	-0.0106	0.0446	0.0219	0.0753	71.1813	60.5573	66.024
9	0.0779	-0.0576	0.1228	0.3495	-0.4853	0.81	0.0031	0.0538	-0.0136	-0.0846	-0.0173	-0.0053	0.0863	0.151	0.0142	0.0719	-0.0206	0.0237	0.1199	-0.0169	0.04	100.106	46.4736	53.576
10	0.4679	-0.2732	-0.2802	0.7435	0.2888	0.3604	0.002	-0.0008	-0.0474	-0.0077	0.0233	-0.0735	0.0377	0.0292	-0.0253	0.0788	0.0177	-0.0356	0.0403	-0.0352	0.0674	83.0698	10.9348	62.9015
11	0.2408	-0.058	-0.2251	0.2738	-0.1026	0.9637	-0.0234	-0.034	-0.0507	-0.0284	0.0281	-0.0134	0.0828	0.1669	-0.0047	0.0352	0.0362	0.0044	0.0896	0.0106	0.0753	100.7196	33.3755	79.4626
12	0.131	-0.12	-0.0535	1.011	-0.1003	0.0903	-0.033	0.0231	-0.0467	-0.1548	0.0385	0.0611	0.0675	0.0331	-0.0056	0.1238	-0.0219	-0.0295	0.0855	-0.0217	0.0392	73.6139	33.4601	56.0682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 230
2	X-RAY DIFFRACTION	2	A	231 - 391
3	X-RAY DIFFRACTION	3	A	392 - 473
4	X-RAY DIFFRACTION	4	B	6 - 221
5	X-RAY DIFFRACTION	5	B	222 - 394
6	X-RAY DIFFRACTION	6	B	395 - 473
7	X-RAY DIFFRACTION	7	C	6 - 230
8	X-RAY DIFFRACTION	8	C	231 - 391
9	X-RAY DIFFRACTION	9	C	392 - 473
10	X-RAY DIFFRACTION	10	D	6 - 230
11	X-RAY DIFFRACTION	11	D	231 - 391
12	X-RAY DIFFRACTION	12	D	392 - 473

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