PDB-5mj7: Structure of the C. elegans nucleoside hydrolase

ID or keywords:

Entry

Database: PDB / ID: 5mj7

Title

Structure of the C. elegans nucleoside hydrolase

Components

Uncharacterized protein

Keywords

HYDROLASE / nucleoside hydrolase / N-ribohydrolase / leaving group activation /

enzyme mechanism

Function / homology

Inosine/uridine-preferring nucleoside hydrolase domain / Inosine-uridine preferring nucleoside hydrolase / Ribonucleoside hydrolase-like /

metal ion binding / IU_nuc_hydro domain-containing protein

Function and homology information

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Versees, W. / Singh, R.K.

Funding support

Belgium, 3items

Citation

Journal: Protein Sci. / Year: 2017
Title: Structural and biochemical characterization of the nucleoside hydrolase from C. elegans reveals the role of two active site cysteine residues in catalysis.
Authors: Singh, R.K. / Steyaert, J. / Versees, W.

History

Deposition	Nov 30, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 8, 2017	Provider: repository / Type: Initial release
Revision 1.1	May 3, 2017	Group: Database references
Revision 1.2	Jul 17, 2019	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	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 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_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.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.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5mj7.cif.gz	280 KB	Display	PDBx/mmCIF format
PDB format	pdb5mj7.ent.gz	227.2 KB	Display	PDB format
PDBx/mmJSON format	5mj7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mj/5mj7 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/5mj7	HTTPS FTP

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Related structure data

Related structure data	3fz0S S: Starting model for refinement
Similar structure data	1ezr-d 1mas-1 6ba0-d 5tsq-1 3mtc-2 2zu0-d 6n0b-d 4cml-1 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

77.4 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

defined by author&software
155 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.578, 84.578, 260.911
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Uncharacterized protein Mass: 38535.133 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: CELE_Y43F8C.13, Y43F8C.13 / Production host: Escherichia coli (E. coli) / Variant (production host): WK6 / References: UniProt: Q9XWN7
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 376 / 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: 3.03 Å³/Da / Density % sol: 59.37 %
Crystal grow	Temperature: 300 K / Method: batch mode / pH: 7.5 / Details: 20 mM Tris, pH 7.5, 150mM NaCl and 2mM DTT

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Data collection

Diffraction	Mean temperature: 300 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8075 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 5, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.8075 Å / Relative weight: 1
Reflection	Resolution: 1.65→24.93 Å / Num. obs: 110218 / % possible obs: 96.2 % / Redundancy: 22.42 % / B_iso Wilson estimate: 26.6 Å² / R_merge(I) obs: 0.071 / Net I/σ(I): 44.9
Reflection shell	Resolution: 1.65→1.71 Å / R_merge(I) obs: 0.579 / Mean I/σ(I) obs: 2.3 / % possible all: 76.2

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: T. b. brucei IG-NH (pdb 3fz0)

3fz0

Resolution: 1.65→24.93 Å / Cor.coef. F_o:F_c: 0.982 / Cor.coef. F_o:F_c free: 0.978 / SU B: 2.419 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.15405	5515	5 %	RANDOM
R_work	0.13722	-	-	-
obs	0.13807	104702	96.1 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å

Displacement parameters

B_iso mean: 25.385 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.02 Å²	0 Å²	0 Å²
2-	-	0.02 Å²	0 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: 1 / Resolution: 1.65→24.93 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4972	0	18	376	5366

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	5170
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	3443
X-RAY DIFFRACTION	r_angle_refined_deg	1.217	1.955	7052
X-RAY DIFFRACTION	r_angle_other_deg	1.011	3	8430
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.712	5	683
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.822	24.159	226
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.98	15	858
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.048	15	29
X-RAY DIFFRACTION	r_chiral_restr	0.092	0.2	809
X-RAY DIFFRACTION	r_gen_planes_refined	0.016	0.02	5838
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1047
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	1.594	1.5	3265
X-RAY DIFFRACTION	r_mcbond_other	0.435	1.5	1328
X-RAY DIFFRACTION	r_mcangle_it	2.903	2	5291
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	4.79	3	1905
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	7.83	4.5	1739
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: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	307	-
R_work	0.301	6038	-
obs	-	-	75.51 %

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	1.0442	0.0815	-0.1337	2.5645	0.4924	0.7984	0.0024	-0.0001	-0.157	0.0604	0.0013	0.148	0.1772	-0.0445	-0.0037	0.2881	-0.025	-0.0039	0.2075	-0.0048	0.2576	10.835	34.405	74.571
2	4.8104	-2.1032	-0.3624	12.0122	5.9765	7.1661	0.0256	0.0144	-0.3074	0.0498	-0.2493	0.7851	0.3589	-0.4836	0.2236	0.2474	-0.1005	-0.0287	0.1788	-0.0418	0.3482	0.199	25.679	69.593
3	5.6161	-0.6632	2.702	0.9478	-0.4336	3.6191	0.0519	-0.3669	-0.1705	0.3357	0.0279	0.1809	0.1332	-0.3021	-0.0798	0.3203	-0.0232	0.0407	0.2027	0.0135	0.2102	8.341	41.49	89.132
4	1.1099	0.1586	-0.2783	1.227	-0.3744	0.8151	0.0026	-0.0471	-0.0643	0.1135	0.0114	-0.0424	0.0051	0.0412	-0.0141	0.2569	-0.0047	-0.0263	0.2048	-0.0112	0.2076	20.394	46.804	76.543
5	0.8813	0.6412	-0.7237	4.0397	-0.0594	0.7519	0.0437	0.1194	-0.0797	-0.2848	0.0424	-0.4145	0.0026	0.098	-0.0861	0.3206	-0.0125	0.0175	0.1559	-0.0594	0.2466	21.516	24.399	64.124
6	17.2064	1.4297	11.2527	-0.0725	3.2107	11.3603	0.341	0.851	0.3827	-1.0716	0.1273	-0.8755	-0.4899	0.3534	-0.4683	0.7471	-0.1115	0.2546	0.2445	-0.0556	0.2033	21.351	30.447	55.358
7	0.8916	0.599	-0.0905	2.1212	-0.2506	1.0086	0.0376	-0.0286	-0.1485	0.1639	-0.0244	-0.2705	0.0714	0.1226	-0.0132	0.2473	0.0099	-0.0268	0.2314	-0.0139	0.238	27.748	44.993	73.497
8	1.1375	1.4392	0.1203	4.9188	0.975	1.4443	0.0339	-0.0441	-0.2521	0.1671	-0.002	-0.3981	0.1564	0.0655	-0.0319	0.2724	0.0223	-0.0572	0.2225	0.0002	0.2816	28.579	32.363	76.023
9	0.9826	-0.6434	-0.5148	1.3799	0.6062	1.9823	-0.0808	-0.194	0.007	0.1836	0.1096	0.0546	0.0324	0.0404	-0.0288	0.2718	0.0149	0.0326	0.2588	0.0141	0.1916	-0.694	69.373	92.328
10	6.1721	-1.255	-0.3869	13.5849	5.1453	6.1198	-0.0686	-0.7568	0.0288	0.971	0.1758	-0.1773	0.4962	0.4058	-0.1072	0.3645	0.0623	0.013	0.3801	0.0053	0.0726	2.622	70.955	106.248
11	4.8805	-0.0454	3.5162	3.093	0.015	4.4951	0.0027	-0.368	-0.5052	0.3944	0.0073	0.3965	0.4548	-0.3277	-0.0101	0.2894	-0.0211	0.104	0.1964	0.0446	0.2758	-4.862	54.219	88.838
12	1.1657	-0.3442	-0.5175	1.2466	-0.1982	1.4361	-0.0241	0.0333	-0.0825	0.0495	0.0275	0.1431	0.0422	-0.1116	-0.0033	0.2143	-0.0094	0.011	0.2259	-0.0038	0.208	-0.481	66.839	76.782
13	0.8144	-0.5829	-0.1211	0.8349	0.3891	2.3178	0.0763	-0.0157	0.2529	-0.0487	0.0453	-0.1294	-0.5376	0.1187	-0.1216	0.2973	-0.0007	0.0795	0.2053	-0.0115	0.2074	-3.559	85.329	89.64
14	4.4922	-3.2909	-3.8427	5.398	4.1612	7.5442	0.2002	0.34	0.0159	-0.086	-0.3282	0.2744	-0.4033	-0.9008	0.128	0.2025	0.0251	-0.023	0.3485	0.0147	0.2542	-10.62	76.001	69.986
15	6.4802	-1.7236	0.8646	4.7627	-1.1992	3.6676	0.1138	0.4485	-0.2914	-0.349	0.0101	0.2997	0.1657	-0.1008	-0.1239	0.2413	-0.0056	0.0006	0.2422	-0.0076	0.2033	5.569	69.623	65.311
16	1.1521	-0.6855	-1.9464	0.621	1.8522	5.7792	0.156	0.1188	0.0833	0.0383	-0.0492	0.0493	-0.2613	-0.5759	-0.1068	0.2678	0.0623	0.053	0.2867	0.0304	0.2042	-13.183	81.242	84.129

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 94
2	X-RAY DIFFRACTION	2	A	95 - 108
3	X-RAY DIFFRACTION	3	A	109 - 126
4	X-RAY DIFFRACTION	4	A	127 - 206
5	X-RAY DIFFRACTION	5	A	207 - 240
6	X-RAY DIFFRACTION	6	A	241 - 250
7	X-RAY DIFFRACTION	7	A	251 - 293
8	X-RAY DIFFRACTION	8	A	294 - 338
9	X-RAY DIFFRACTION	9	B	5 - 94
10	X-RAY DIFFRACTION	10	B	95 - 108
11	X-RAY DIFFRACTION	11	B	109 - 124
12	X-RAY DIFFRACTION	12	B	125 - 206
13	X-RAY DIFFRACTION	13	B	207 - 264
14	X-RAY DIFFRACTION	14	B	265 - 276
15	X-RAY DIFFRACTION	15	B	277 - 310
16	X-RAY DIFFRACTION	16	B	311 - 338

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