PDB-5h7w: Crystal structure of 5'-nucleotidase from venom of Naja atra

ID or keywords:

Entry

Database: PDB / ID: 5h7w

Title

Crystal structure of 5'-nucleotidase from venom of Naja atra

Components

venom 5'-nucleotidase

Keywords

HYDROLASE /

5'-nucleotidase / purine hydrolysis /

snake venom protein

Function / homology

Function and homology information

: / nucleotide catabolic process /

5'-nucleotidase /

5'-nucleotidase activity /

nucleotide binding /

metal ion binding
Similarity search - Function

Biological species

Naja atra (Chinese cobra)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.9 Å

Authors

Chang, C. / Lin, C.-C. / Wu, W.-G.

Funding support

Taiwan, 1items

Citation

Journal: To Be Published
Title: Crystal strucuture of Taiwan cobra (Naja atra) venom 5'-nucleotidase at 1.9 Angstroms resolution.
Authors: Chang, C. / Lin, C.-C. / Wu, W.-G.

History

Deposition	Nov 21, 2016	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 22, 2017	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_conn_type.id Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5h7w.cif.gz	430.4 KB	Display	PDBx/mmCIF format
PDB format	pdb5h7w.ent.gz	355.5 KB	Display	PDB format
PDBx/mmJSON format	5h7w.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/h7/5h7w ftp://data.pdbj.org/pub/pdb/validation_reports/h7/5h7w	HTTPS FTP

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Related structure data

Similar structure data	2zsm-d 22357 4rmn-d 7kc4-d 6tve-1 2zw4-d 4nhe-d 7bsj-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	#225 - Sep 2018 Phytase similarity (3)

Deposited unit

A: venom 5'-nucleotidase

B: venom 5'-nucleotidase

hetero molecules

118 kDa, 2 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)	53.089, 68.149, 139.815
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, 2 molecules AB

#1: Protein	venom 5'-nucleotidase Mass: 58268.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Naja atra (Chinese cobra) / References: UniProt: A0A2I4HXH5*PLUS

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Sugars , 2 types, 3 molecules

#2: Polysaccharide

beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...

Type: oligosaccharide

/ Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source

Descriptor	Type	Program
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1	WURCS	PDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}	LINUCS	PDB-CARE

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose /

N-Acetylglucosamine

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

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Non-polymers , 3 types, 960 molecules

#4: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 954 / 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: 2.16 Å³/Da / Density % sol: 43.06 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M calcium acetate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. obs: 88970 / % possible obs: 93 % / Redundancy: 6.5 % / R_merge(I) obs: 0.076 / Net I/σ(I): 22.9
Reflection shell	Resolution: 1.9→1.97 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.754 / Mean I/σ(I) obs: 2.6 / % possible all: 89.4

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
HKL-2000		data collection
HKL-2000		data scaling
Coot		model building
PHASER		phasing

Refinement

Resolution: 1.9→24.98 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.87 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.197	3492	4.91 %
R_work	0.155	-	-
obs	0.157	71082	90.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.9→24.98 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8178	0	98	954	9230

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8475
X-RAY DIFFRACTION	f_angle_d	1.136	11490
X-RAY DIFFRACTION	f_dihedral_angle_d	17.711	5072
X-RAY DIFFRACTION	f_chiral_restr	0.066	1297
X-RAY DIFFRACTION	f_plane_restr	0.006	1487

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.8966-1.9226	0.2777	86	0.2073	1725	X-RAY DIFFRACTION	58
1.9226-1.9501	0.251	115	0.2004	2143	X-RAY DIFFRACTION	72
1.9501-1.9792	0.2434	118	0.1975	2270	X-RAY DIFFRACTION	77
1.9792-2.0101	0.2611	128	0.1944	2482	X-RAY DIFFRACTION	83
2.0101-2.043	0.2568	130	0.1885	2602	X-RAY DIFFRACTION	87
2.043-2.0782	0.2315	135	0.1871	2627	X-RAY DIFFRACTION	89
2.0782-2.116	0.2311	137	0.1809	2674	X-RAY DIFFRACTION	88
2.116-2.1567	0.229	139	0.1795	2618	X-RAY DIFFRACTION	89
2.1567-2.2007	0.2827	143	0.1689	2668	X-RAY DIFFRACTION	89
2.2007-2.2485	0.2105	146	0.1686	2656	X-RAY DIFFRACTION	89
2.2485-2.3008	0.2329	145	0.1599	2695	X-RAY DIFFRACTION	91
2.3008-2.3582	0.2402	135	0.1601	2713	X-RAY DIFFRACTION	91
2.3582-2.422	0.2013	145	0.16	2733	X-RAY DIFFRACTION	91
2.422-2.4932	0.2083	123	0.1571	2775	X-RAY DIFFRACTION	93
2.4932-2.5736	0.1793	152	0.1562	2752	X-RAY DIFFRACTION	92
2.5736-2.6654	0.1711	126	0.1527	2825	X-RAY DIFFRACTION	93
2.6654-2.772	0.2103	151	0.1666	2820	X-RAY DIFFRACTION	95
2.772-2.898	0.2322	137	0.1644	2869	X-RAY DIFFRACTION	96
2.898-3.0506	0.2112	156	0.1565	2895	X-RAY DIFFRACTION	96
3.0506-3.2413	0.189	150	0.1484	2926	X-RAY DIFFRACTION	97
3.2413-3.4909	0.1736	202	0.1425	2915	X-RAY DIFFRACTION	99
3.4909-3.8411	0.1713	134	0.1353	3021	X-RAY DIFFRACTION	99
3.8411-4.3943	0.1563	152	0.1243	3023	X-RAY DIFFRACTION	100
4.3943-5.5265	0.1555	149	0.1345	3045	X-RAY DIFFRACTION	100
5.5265-24.9772	0.193	158	0.1639	3118	X-RAY DIFFRACTION	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	3.1926	-0.6823	0.8902	3.0073	-0.8119	2.9723	-0.0049	0.0394	0.2758	-0.0815	-0.0668	-0.1919	-0.2761	0.0691	0.0637	0.1398	-0.0214	0.0069	0.0867	-0.0117	0.1218	13.5504	30.301	14.3644
2	3.2642	-0.8259	0.8415	1.6092	0.3437	1.8475	-0.0759	-0.6815	0.0313	0.3272	0.0513	0.2832	-0.0514	-0.5553	0.0172	0.203	0.0056	0.0349	0.3589	-0.0167	0.1588	-2.2275	24.1903	24.6364
3	2.1316	-0.2632	0.4722	1.832	0.0339	2.0189	0.0021	0.2147	0.096	-0.1978	-0.0223	0.1486	-0.0737	-0.3057	0.0191	0.1509	0.0203	-0.0047	0.1784	0.0132	0.1085	0.1284	26.1635	5.3449
4	0.6825	-1.0879	0.4239	2.16	-0.5092	0.3317	-0.0759	-0.0858	0.1695	0.1604	0.0756	-0.2832	-0.0885	0.0165	-0.0006	0.1739	-0.0407	0.028	0.2197	-0.0171	0.1957	30.5722	14.8839	24.0479
5	8.6644	3.2377	1.8117	6.0526	0.1155	4.5867	0.0325	-0.3351	0.4248	0.2695	0.0478	0.7854	-0.0916	-0.5022	-0.0807	0.1465	-0.0005	0.0142	0.1347	0.0275	0.1326	12.5389	0.9923	26.5123
6	1.2579	0.2099	0.0112	1.3716	-0.1942	1.2167	-0.0527	0.1293	-0.0636	-0.2152	0.053	0.0257	0.1248	-0.1041	-0.0011	0.1629	-0.0205	0.0142	0.1056	-0.001	0.086	19.8848	-2.1451	15.4787
7	2.9258	0.3796	0.8154	5.9129	0.2981	2.615	0.0067	-0.2231	-0.0439	0.359	-0.0368	-0.1458	0.1132	-0.0131	0.0307	0.0705	-0.0325	0.0338	0.1313	0.0321	0.071	25.576	-1.1193	26.838
8	2.824	-0.0006	0.9899	1.4839	-0.0464	3.184	-0.0181	-0.1063	0.0036	0.0752	-0.0304	0.1813	0.0399	-0.2637	0.0594	0.0672	0.0132	0.0196	0.0847	-0.0159	0.15	27.3111	1.6709	72.0369
9	3.4895	-0.0604	1.6787	1.2362	-0.1262	2.1493	-0.0632	0.3031	0.1743	-0.1178	0.0123	-0.1268	-0.1187	0.2044	0.0432	0.0929	-0.0155	0.0217	0.1091	0.0057	0.1282	44.2029	4.5094	63.0011
10	0.7234	0.294	0.6575	0.2752	0.2651	1.2142	0.0358	-0.0712	-0.0443	0.0352	-0.0069	-0.0358	0.0133	-0.0927	-0.028	0.0957	-0.0136	0.0219	0.0911	0.0188	0.1584	28.3365	-5.7843	68.3941
11	1.4834	-0.1052	-0.3757	1.4972	0.0234	2.188	-0.0322	-0.2205	-0.1386	0.1014	-0.0287	-0.1157	0.1111	0.1727	0.0421	0.1257	0.0009	-0.0117	0.1348	0.0331	0.092	25.255	-15.231	43.4596
12	3.1388	-1.3467	-0.3605	4.8642	1.0549	4.9373	0.0433	0.0692	0.0595	-0.3345	-0.072	0.1355	-0.0739	-0.1284	0.0313	0.0435	-0.0104	0.034	0.1475	0.0578	0.0957	17.0927	-8.5952	38.364

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 26 THROUGH 107 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 108 THROUGH 209 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 210 THROUGH 317 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 318 THROUGH 358 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 359 THROUGH 386 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 387 THROUGH 524 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 525 THROUGH 553 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 26 THROUGH 108 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 109 THROUGH 245 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 246 THROUGH 358 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 359 THROUGH 524 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 525 THROUGH 554 )

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