PDB-5jxw: 2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from ...

ID or keywords:

Entry

Database: PDB / ID: 5jxw

Title

2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Neplanocin-A and NAD

Components

Adenosylhomocysteinase

Keywords

HYDROLASE / S-adenosylhomocysteinase / Neplanocin-A / NAD / 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: 2.25 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: 2.25 Angstrom Crystal Structure of S-adenosylhomocysteinase from Cryptosporidium parvum in Complex with Neplanocin-A 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	May 13, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 25, 2016	Provider: repository / Type: Initial release
Revision 1.1	Aug 24, 2016	Group: Other
Revision 1.2	Sep 27, 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_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	5jxw.cif.gz	787.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5jxw.ent.gz	656 KB	Display	PDB format
PDBx/mmJSON format	5jxw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5jxw_validation.pdf.gz	2.8 MB	Display	wwPDB validaton report
Full document	5jxw_full_validation.pdf.gz	2.9 MB	Display
Data in XML	5jxw_validation.xml.gz	75.8 KB	Display
Data in CIF	5jxw_validation.cif.gz	105.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jx/5jxw ftp://data.pdbj.org/pub/pdb/validation_reports/jx/5jxw	HTTPS FTP

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Related structure data

Related structure data	5hm8S 5jpi S: Starting model for refinement
Similar structure data	5tls-d 5jpi-d 5t8k-d 5utu-1 5hm8-2 5tj9-d 5hm8-1 5utu-2 1v8b-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
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

230 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)	70.885, 136.486, 107.805
Angle α, β, γ (deg.)	90.00, 95.73, 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 (eukaryote) / 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 , 6 types, 771 molecules

#2: Chemical	ChemComp-6OS / Neplanocin-A / (1S,2R,5R)-5-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)cyclopent-3-ene-1,2-diol Mass: 263.253 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Formula: C₁₁H₁₃N₅O₃
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 754 / 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: 2.32 Å³/Da / Density % sol: 46.9 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein: 9.3 mg/ml, 0.1M Tris HCl (pH 8.3),1mM NeplanocinA; Screen: Classics II (D7), 0.1M Bis-Tris-HCL (pH 6.5), 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-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2016 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.25→30 Å / Num. obs: 96622 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / B_iso Wilson estimate: 41.6 Å² / CC_1/2: 0.87 / R_merge(I) obs: 0.078 / R_sym value: 0.078 / Net I/σ(I): 17.1
Reflection shell	Resolution: 2.25→2.29 Å / Redundancy: 4.2 % / R_merge(I) obs: 0.662 / Mean I/σ(I) obs: 2.5 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0135	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB-5HM8

5hm8

Resolution: 2.25→29.93 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.943 / SU B: 13.603 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.323 / ESU R Free: 0.216 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22103	4857	5 %	RANDOM
R_work	0.17341	-	-	-
obs	0.1758	91403	99.64 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 48.575 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.12 Å²	0 Å²	4.32 Å²
2-	-	-2.58 Å²	0 Å²
3-	-	-	-1.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→29.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15383	0	338	754	16475

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	16106
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	15621
X-RAY DIFFRACTION	r_angle_refined_deg	1.469	1.996	21760
X-RAY DIFFRACTION	r_angle_other_deg	0.893	3	36077
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.852	5	1965
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.13	25.206	680
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.998	15	3006
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.169	15	68
X-RAY DIFFRACTION	r_chiral_restr	0.086	0.2	2469
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.02	17750
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	3418
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	1.6	2.822	7851
X-RAY DIFFRACTION	r_mcbond_other	1.599	2.82	7847
X-RAY DIFFRACTION	r_mcangle_it	2.667	4.223	9817
X-RAY DIFFRACTION	r_mcangle_other	2.666	4.223	9818
X-RAY DIFFRACTION	r_scbond_it	1.794	3.148	8255
X-RAY DIFFRACTION	r_scbond_other	1.794	3.148	8255
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.91	4.609	11944
X-RAY DIFFRACTION	r_long_range_B_refined	6.389	23.613	19130
X-RAY DIFFRACTION	r_long_range_B_other	6.36	23.328	18871
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.25→2.308 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.432	384	-
R_work	0.391	6561	-
obs	-	-	98.05 %

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	2.9976	0.7883	0.2992	1.0694	0.5703	1.563	0.1666	-0.1432	-0.4452	0.2944	-0.0174	-0.1678	0.2475	0.2524	-0.1492	0.1388	0.018	-0.1296	0.2243	0.0328	0.2217	-26.1822	-31.8306	8.3007
2	1.8185	-0.1325	-0.6282	1.8808	0.1318	2.023	0.005	-0.1071	-0.0027	0.1726	-0.0253	0.2796	0.1287	-0.1366	0.0203	0.0381	-0.0095	-0.0139	0.1501	-0.0055	0.1605	-49.137	-23.9152	9.7112
3	0.3496	0.0232	-0.3993	0.8735	0.3165	0.6097	0.0556	0.0446	0.0306	-0.0297	0.0085	0.0249	-0.0688	0.0154	-0.064	0.041	0.0178	-0.0708	0.2896	0.005	0.2025	-30.5402	-22.8939	-15.5885
4	1.3577	0.5898	-0.0939	1.5463	0.5732	1.3564	0.0598	0.0638	-0.0628	0.1165	-0.0673	0.196	0.0982	-0.2031	0.0075	0.0457	-0.0035	-0.0807	0.336	-0.001	0.285	-39.7993	-37.3491	-18.0507
5	0.6681	0.5578	-0.5538	0.8621	-0.7391	0.6596	0.1308	-0.0672	0.106	0.147	-0.0535	0.0334	-0.1223	0.0832	-0.0773	0.0799	-0.0092	-0.0687	0.2421	-0.0392	0.1707	-17.0756	-10.3811	-1.9178
6	1.7693	0.4769	0.2877	1.6079	0.5211	0.8412	-0.1001	0.2173	0.243	-0.4129	0.0708	0.0707	-0.2598	-0.0071	0.0294	0.1822	0.021	-0.0377	0.1747	0.0829	0.0961	-20.6624	11.7333	-38.3142
7	1.5202	-0.4261	-1.1428	3.2229	1.4453	1.5413	-0.1562	-0.0402	0.0457	-0.1776	0.2039	-0.2673	-0.1009	0.3228	-0.0476	0.2218	-0.0325	-0.0425	0.2569	0.0316	0.1418	-7.7882	24.6678	-20.6743
8	0.3194	-0.3133	-0.1118	1.4763	0.0331	0.3238	0.0347	0.0067	0.0333	-0.1161	0.0195	-0.1563	-0.0977	0.0101	-0.0541	0.0524	-0.0068	-0.0135	0.201	-0.0042	0.1545	-10.4842	-7.6525	-22.0373
9	1.9436	-0.4844	-0.272	1.2628	0.1505	0.3943	0.0163	0.0488	0.1417	-0.1637	0.0097	-0.2956	-0.1233	0.0659	-0.026	0.0572	-0.0277	0.0268	0.1509	0.0234	0.1457	-1.5423	-1.4968	-29.2008
10	0.3496	0.55	-0.0554	2.6117	-0.1223	0.0413	0.0801	0.0078	0.0071	-0.0749	-0.021	0.2798	-0.068	-0.087	-0.0591	0.2127	0.1155	-0.022	0.4062	0.0469	0.3089	-36.2755	-5.668	-21.2443
11	1.1623	-0.4252	0.5201	0.6674	0.1743	2.0716	0.0409	0.1457	0.0986	-0.3162	0.1646	-0.2748	-0.6183	0.5618	-0.2055	0.316	-0.1813	0.1434	0.3598	-0.0499	0.1998	10.8661	-20.0452	-56.8816
12	3.1462	-1.2871	-0.0236	2.4231	-0.9997	3.9306	0.3383	0.3237	-0.0328	-0.5289	0.0007	-0.0448	-0.1229	0.0387	-0.339	0.1926	0.0088	0.0274	0.1639	-0.009	0.0508	-0.6374	-29.5415	-77.072
13	0.7381	-0.27	-0.4483	0.6251	0.3214	1.0501	0.0732	0.0455	-0.0174	-0.2154	0.025	0.0148	-0.1726	-0.017	-0.0982	0.1076	0.0191	-0.0423	0.2639	0.009	0.1264	-11.6269	-29.7098	-46.34
14	2.0676	-0.7251	0.4041	1.6814	0.1615	1.9433	0.2011	0.3229	0.1704	-0.343	-0.0771	0.1441	-0.5157	-0.2279	-0.124	0.27	0.1108	-0.0211	0.2627	0.0926	0.1193	-19.5425	-17.2504	-55.0375
15	0.5072	0.2508	-0.2078	0.5752	-0.6992	2.2179	0.0717	0.0321	-0.1117	-0.0683	0.0564	-0.1904	0.0216	0.3148	-0.1282	0.0753	-0.0063	-0.025	0.3943	-0.075	0.2931	8.7536	-39.2088	-40.2328
16	0.9413	-0.6213	-0.0614	1.479	0.1188	1.0008	-0.0728	-0.0398	-0.1005	0.0941	-0.0082	0.2127	0.2071	-0.077	0.081	0.0883	-0.0133	-0.0583	0.275	0.0122	0.2143	-20.1341	-65.6917	-24.1974
17	1.8295	-0.4874	-0.7932	7.0925	1.9324	3.7482	-0.1369	-0.3526	0.0445	0.9095	0.2602	-0.3555	0.5817	0.4731	-0.1233	0.1819	0.0929	-0.0888	0.2475	0.0281	0.1053	2.1753	-73.4572	-15.5102
18	0.1695	-0.0815	-0.2156	1.6397	0.4067	0.8886	0.0106	-0.0358	-0.0109	0.019	-0.0063	-0.0819	-0.0199	0.0927	-0.0043	0.0409	0.0282	-0.0883	0.3283	-0.0036	0.207	-4.5992	-45.0955	-22.9306
19	0.6769	0.4084	1.0058	1.4808	1.0272	2.6566	0.0439	-0.043	-0.1345	0.295	0.0391	-0.0009	0.1102	0.0179	-0.083	0.1193	0.0043	-0.0846	0.3251	0.0222	0.1809	-8.5444	-48.5092	-11.9012
20	0.276	-0.1989	-0.0709	1.4977	-0.5549	0.4162	0.0085	0.1021	-0.047	-0.3671	-0.007	0.0793	0.1534	-0.043	-0.0015	0.128	0.0235	-0.0778	0.321	-0.0358	0.1504	-16.3303	-49.4328	-47.1129

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 119
2	X-RAY DIFFRACTION	2	A	120 - 204
3	X-RAY DIFFRACTION	3	A	205 - 322
4	X-RAY DIFFRACTION	4	A	323 - 412
5	X-RAY DIFFRACTION	5	A	413 - 495
6	X-RAY DIFFRACTION	6	B	3 - 144
7	X-RAY DIFFRACTION	7	B	145 - 206
8	X-RAY DIFFRACTION	8	B	207 - 333
9	X-RAY DIFFRACTION	9	B	334 - 430
10	X-RAY DIFFRACTION	10	B	431 - 495
11	X-RAY DIFFRACTION	11	C	3 - 147
12	X-RAY DIFFRACTION	12	C	148 - 206
13	X-RAY DIFFRACTION	13	C	207 - 322
14	X-RAY DIFFRACTION	14	C	323 - 412
15	X-RAY DIFFRACTION	15	C	413 - 495
16	X-RAY DIFFRACTION	16	D	-2 - 157
17	X-RAY DIFFRACTION	17	D	158 - 197
18	X-RAY DIFFRACTION	18	D	198 - 357
19	X-RAY DIFFRACTION	19	D	358 - 426
20	X-RAY DIFFRACTION	20	D	427 - 495

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Yorodumi