PDB-5tj9: 2.6 Angstrom Crystal Structure of S-adenosylhomocysteinase from C...

ID or keywords:

Entry

Database: PDB / ID: 5tj9

Title

2.6 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Aristeromycin and NAD

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

adenosylhomocysteinase / adenosylhomocysteinase activity / S-adenosylmethionine cycle / one-carbon metabolic process / nucleotide binding / cytosol
Similarity search - Function

Biological species

Cryptosporidium parvum (eukaryote)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.6 Å

Authors

Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 2.6 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Aristeromycin and NAD
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Bishop, B. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Oct 4, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 19, 2016	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5tj9.cif.gz	789.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5tj9.ent.gz	659.3 KB	Display	PDB format
PDBx/mmJSON format	5tj9.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5tj9_validation.pdf.gz	3 MB	Display	wwPDB validaton report
Full document	5tj9_full_validation.pdf.gz	3.1 MB	Display
Data in XML	5tj9_validation.xml.gz	70.9 KB	Display
Data in CIF	5tj9_validation.cif.gz	96.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tj/5tj9 ftp://data.pdbj.org/pub/pdb/validation_reports/tj/5tj9	HTTPS FTP

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Related structure data

Related structure data	5hm8S 5jpi 5jxw 5t8k S: Starting model for refinement
Similar structure data	5tls-d 5utu-1 5t8k-d 5hm8-2 5jxw-d 5utu-2 5jpi-d 5hm8-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: CSGID-IDP95479

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Adenosylhomocysteinase

B: Adenosylhomocysteinase

C: Adenosylhomocysteinase

D: Adenosylhomocysteinase

hetero molecules

231 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)	66.331, 184.904, 102.508
Angle α, β, γ (deg.)	90.00, 107.80, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	Adenosylhomocysteinase Mass: 56200.676 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cryptosporidium parvum (strain Iowa II) (eukaryote) Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q5CPH1, adenosylhomocysteinase

#1: Protein

Adenosylhomocysteinase

Mass: 56200.676 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Cryptosporidium parvum (strain Iowa II) (eukaryote)
Strain: Iowa II / Gene: cgd3_80 / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q5CPH1, adenosylhomocysteinase

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Non-polymers , 7 types, 408 molecules

#2: Chemical	ChemComp-7CY / (1R,2S,3R,5R)-3-(6-amino-9H-purin-9-yl)-5-(hydroxymethyl)cyclopentane-1,2-diol / Aristeromycin Mass: 265.269 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₁H₁₅N₅O₃
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#4: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO₄
#5: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Comment: precipitant*YM
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.67 Å³/Da / Density % sol: 54 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3), 1mM NAD, 1mM Aristeromycin; Screen: Classics II (F9), 0.2M Ammonium sulfate, 0.1M Tris-HCL (pH 8.5), 25% (w/v) PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2016 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97856 Å / Relative weight: 1
Reflection	Resolution: 2.6→30 Å / Num. obs: 72106 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / B_iso Wilson estimate: 55.9 Å² / R_merge(I) obs: 0.095 / R_sym value: 0.095 / Net I/σ(I): 14.5
Reflection shell	Resolution: 2.6→2.64 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.684 / Mean I/σ(I) obs: 2.1 / CC_1/2: 0.704 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0155	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5HM8

5hm8

Resolution: 2.6→29.88 Å / Cor.coef. F_o:F_c: 0.962 / Cor.coef. F_o:F_c free: 0.934 / SU B: 21.531 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 1.153 / ESU R Free: 0.284 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2183	3741	5.2 %	RANDOM
R_work	0.1681	-	-	-
obs	0.17064	68278	99.91 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 56.924 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.34 Å²	0 Å²	0.87 Å²
2-	-	0.16 Å²	0 Å²
3-	-	-	1.34 Å²

Refinement step

Cycle: 1 / Resolution: 2.6→29.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15624	0	383	381	16388

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	16345
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	15861
X-RAY DIFFRACTION	r_angle_refined_deg	1.452	2	22081
X-RAY DIFFRACTION	r_angle_other_deg	0.899	3	36612
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.213	5	1988
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	26.815	25.152	689
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.14	15	3061
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	6.956	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	2515
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	17964
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	3472
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	1.67	3.969	7943
X-RAY DIFFRACTION	r_mcbond_other	1.67	3.969	7942
X-RAY DIFFRACTION	r_mcangle_it	2.844	5.95	9934
X-RAY DIFFRACTION	r_mcangle_other	2.844	5.95	9935
X-RAY DIFFRACTION	r_scbond_it	1.78	4.265	8402
X-RAY DIFFRACTION	r_scbond_other	1.78	4.265	8402
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.969	6.28	12148
X-RAY DIFFRACTION	r_long_range_B_refined	4.866	46.685	18349
X-RAY DIFFRACTION	r_long_range_B_other	4.858	46.636	18296
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.6→2.667 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	263	-
R_work	0.26	5012	-
obs	-	-	99.87 %

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	2.2244	0.5953	-0.5902	1.7452	-0.0683	2.1114	0.0124	-0.4939	-0.01	0.3569	0.0039	-0.1624	0.0448	0.3222	-0.0163	0.1636	-0.024	-0.084	0.2529	0.0032	0.0467	72.9976	33.0809	53.1327
2	0.538	0.0313	-0.2322	0.4929	-0.1352	1.2113	0.1326	-0.2621	0.1231	0.2096	0.0556	-0.065	-0.3017	-0.091	-0.1882	0.2038	-0.0292	0.0192	0.2157	-0.0491	0.0648	56.9147	43.0138	57.0309
3	1.1391	0.6453	-0.0804	1.7826	0.0017	1.4721	0.0684	-0.2108	-0.0178	0.1783	-0.0115	0.1003	0.0436	-0.1827	-0.057	0.0751	-0.012	-0.0084	0.1292	0.0257	0.0902	45.6669	25.8734	37.0405
4	0.5051	-0.1934	-0.2097	0.1334	-0.1876	1.4245	0.0666	-0.1059	0.2245	0.0719	0.006	-0.0839	-0.4132	0.2484	-0.0726	0.231	-0.085	-0.0334	0.0977	-0.0437	0.2275	70.9689	48.7184	36.5223
5	1.7186	0.0759	-0.7349	1.4863	-0.042	1.2582	-0.0284	0.1908	0.1734	-0.1118	0.0839	0.271	-0.2073	-0.2149	-0.0554	0.192	0.0658	-0.0293	0.0642	0.0634	0.2596	45.121	59.9947	1.4237
6	0.2387	0.202	-0.1894	1.9793	-0.2157	0.7011	0.0805	-0.0429	0.1071	0.1119	-0.0983	0.0688	-0.2623	-0.0017	0.0178	0.2328	0.0177	-0.0072	0.0237	0.0125	0.2505	60.3702	69.5446	8.049
7	1.356	-0.3571	-0.5878	1.2956	-0.0593	2.2513	0.105	0.0994	0.2011	-0.0666	-0.0796	-0.1181	-0.139	-0.0425	-0.0254	0.1038	-0.0087	-0.0002	0.0247	0.052	0.1259	73.1413	43.5749	5.2942
8	0.4539	0.0507	-0.0246	0.8542	-0.5768	1.0528	0.0236	-0.1343	0.2059	0.132	0.0582	0.2076	-0.2356	-0.0793	-0.0818	0.1438	0.042	0.0257	0.0721	-0.0207	0.1917	47.7246	54.834	22.3324
9	2.2266	-0.0438	0.1409	2.1742	-0.087	1.7633	-0.0249	0.5417	0.1455	-0.3706	0.0482	0.0106	-0.0375	0.0459	-0.0233	0.1631	0.0022	-0.026	0.1852	0.0381	0.0166	62.7284	26.0476	-20.4924
10	1.68	0.2544	0.6975	1.4684	0.2959	2.4557	0.046	0.3017	-0.1371	-0.407	0.096	0.1987	0.3491	-0.3693	-0.142	0.2658	-0.0673	-0.1272	0.2007	-0.0149	0.0772	48.191	10.5767	-22.0555
11	1.4401	-0.3408	-0.1362	1.2772	-0.3154	0.7329	0.0921	0.1854	0.0861	-0.0484	0.0159	0.1526	-0.0193	-0.1821	-0.1079	0.1008	0.0033	-0.0576	0.1199	0.0323	0.1154	41.955	27.8017	3.0685
12	0.6545	-0.0686	0.1359	0.5267	-0.3626	1.3184	0.0447	0.1231	-0.2408	-0.1632	-0.0248	0.0484	0.3002	0.1766	-0.0199	0.1683	0.0365	-0.0349	0.0657	-0.0359	0.1163	69.2264	10.3998	-4.3671
13	2.8197	0.4432	0.4909	1.5178	0.102	1.5564	0.0137	-0.3653	-0.2364	0.283	-0.0201	0.1132	0.2115	-0.1081	0.0064	0.2406	-0.0532	0.0217	0.0809	0.0795	0.1674	57.6849	-4.8478	36.4602
14	0.744	0.0647	0.2509	1.5632	-0.1779	2.5566	-0.039	-0.0878	-0.2739	0.0737	-0.0235	-0.2054	0.4809	0.2016	0.0625	0.2516	0.0176	0.0023	0.04	0.0581	0.3364	73.2176	-14.3038	25.1927
15	1.4467	0.2798	0.2551	0.8765	0.0394	1.2566	0.0625	-0.1015	-0.0613	0.0595	-0.063	-0.0361	0.0264	0.1103	0.0005	0.1132	-0.005	-0.0429	0.069	0.0312	0.1149	77.086	16.731	25.6625
16	0.3185	0.0085	-0.3833	0.5697	-0.0888	0.5417	-0.0733	0.1044	-0.1266	-0.1155	0.0511	0.2226	0.1345	-0.1458	0.0222	0.2273	-0.0688	-0.0465	0.1067	-0.0143	0.2744	51.1262	-0.4566	14.5221

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 119
2	X-RAY DIFFRACTION	2	A	120 - 261
3	X-RAY DIFFRACTION	3	A	262 - 400
4	X-RAY DIFFRACTION	4	A	401 - 495
5	X-RAY DIFFRACTION	5	B	2 - 119
6	X-RAY DIFFRACTION	6	B	120 - 260
7	X-RAY DIFFRACTION	7	B	261 - 395
8	X-RAY DIFFRACTION	8	B	396 - 495
9	X-RAY DIFFRACTION	9	C	1 - 119
10	X-RAY DIFFRACTION	10	C	120 - 246
11	X-RAY DIFFRACTION	11	C	247 - 401
12	X-RAY DIFFRACTION	12	C	402 - 495
13	X-RAY DIFFRACTION	13	D	1 - 119
14	X-RAY DIFFRACTION	14	D	120 - 243
15	X-RAY DIFFRACTION	15	D	244 - 402
16	X-RAY DIFFRACTION	16	D	403 - 495

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