PDB-4xba: Hnt3 - Yorodumi

ID or keywords:

Entry

Database: PDB / ID: 4xba

Title

Hnt3

Components

Aprataxin-like protein

Keywords

HYDROLASE / GMP /

nucleotidyl transferase

Function / homology

Function and homology information

guanosine binding / adenosine-5'-diphospho-5'-[DNA] diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA-3'-diphospho-5'-guanosine diphosphatase / DNA 5'-adenosine monophosphate hydrolase activity / GMP binding / single-strand break-containing DNA binding / single strand break repair / mismatched DNA binding /

mismatch repair ...
Similarity search - Function

Biological species

Schizosaccharomyces pombe (fission yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Jacewicz, A. / Chauleau, M. / Shuman, S.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2015
Title: DNA3'pp5'G de-capping activity of aprataxin: effect of cap nucleoside analogs and structural basis for guanosine recognition.
Authors: Chauleau, M. / Jacewicz, A. / Shuman, S.

History

Deposition	Dec 16, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 3, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jun 10, 2015	Group: Database references
Revision 1.2	Jul 22, 2015	Group: Database references
Revision 1.3	Jul 27, 2016	Group: Data collection
Revision 1.4	Sep 13, 2017	Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5	Dec 25, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6	Sep 27, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4xba.cif.gz	188.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4xba.ent.gz	147.2 KB	Display	PDB format
PDBx/mmJSON format	4xba.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/xb/4xba ftp://data.pdbj.org/pub/pdb/validation_reports/xb/4xba	HTTPS FTP

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Related structure data

Related structure data	4yklC 3szqS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tsj-2 5d79-2 4lev-1 3tsj-1 6bza-4 3mzo-3 1rxw-d 5fjn-1 6bzz-3 6b4h-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#104 - Aug 2008 Selenocysteine Synthase similarity (1) #151 - Jul 2012 Hypoxanthine-guanine phosphoribosyltransferase similarity (1) #145 - Jan 2012 Messenger RNA Capping similarity (1) #245 - May 2020 Spliceosomes similarity (1) #86 - Feb 2007 Exosomes similarity (1)

Deposited unit

A: Aprataxin-like protein

B: Aprataxin-like protein

hetero molecules

47.3 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)	52.761, 72.509, 53.926
Angle α, β, γ (deg.)	90.00, 111.25, 90.00
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 2 molecules AB

#1: Protein	Aprataxin-like protein / Hit family protein 3 Mass: 23226.652 Da / Num. of mol.: 2 / Fragment: UNP residues 33-232 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast) Strain: 972 / ATCC 24843 / Gene: hnt3, SPCC18.09c / Plasmid: pet28b-His10-Smt3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O74859, Hydrolases

#1: Protein

Aprataxin-like protein / Hit family protein 3

Mass: 23226.652 Da / Num. of mol.: 2 / Fragment: UNP residues 33-232
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: hnt3, SPCC18.09c / Plasmid: pet28b-His10-Smt3 / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O74859,

Hydrolases

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Non-polymers , 5 types, 362 molecules

#2: Chemical	ChemComp-GMP / GUANOSINE / Guanosine Mass: 283.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₃N₅O₅
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate Mass: 363.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₄N₅O₈P
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.07 Å³/Da / Density % sol: 41 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 16%(w/v) PEG3350, 0.15 M Li2SO4, 0.1 M Tris-HCl, pH 8.0 PH range: 8

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 20, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.5→72.51 Å / Num. obs: 59945 / % possible obs: 99 % / Redundancy: 6.6 % / R_merge(I) obs: 0.07 / R_sym value: 0.07 / Net I/σ(I): 13.4
Reflection shell	Resolution: 1.5→1.58 Å / Redundancy: 6.6 % / R_merge(I) obs: 0.831 / Mean I/σ(I) obs: 2.5 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8.4_1496)	refinement
XDS		data reduction
SCALA		data scaling
Coot		model building
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SZQ

3szq

Resolution: 1.5→50.261 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.81 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1912	2950	4.92 %	Random selection
R_work	0.1574	-	-	-
obs	0.1591	59915	98.92 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.5→50.261 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3190	0	52	357	3599

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	3452
X-RAY DIFFRACTION	f_angle_d	1.569	4710
X-RAY DIFFRACTION	f_dihedral_angle_d	13.25	1297
X-RAY DIFFRACTION	f_chiral_restr	0.078	521
X-RAY DIFFRACTION	f_plane_restr	0.008	591

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 (%)
1.5-1.5246	0.3489	159	0.3262	2655	X-RAY DIFFRACTION	99
1.5246-1.5509	0.348	172	0.3018	2698	X-RAY DIFFRACTION	99
1.5509-1.5791	0.2883	139	0.2779	2724	X-RAY DIFFRACTION	99
1.5791-1.6095	0.2458	151	0.2484	2666	X-RAY DIFFRACTION	99
1.6095-1.6423	0.3044	157	0.2391	2687	X-RAY DIFFRACTION	98
1.6423-1.678	0.2317	143	0.2157	2664	X-RAY DIFFRACTION	98
1.678-1.7171	0.2629	102	0.1964	2751	X-RAY DIFFRACTION	99
1.7171-1.76	0.2425	149	0.1746	2736	X-RAY DIFFRACTION	100
1.76-1.8076	0.25	143	0.1668	2729	X-RAY DIFFRACTION	100
1.8076-1.8608	0.2054	113	0.1636	2708	X-RAY DIFFRACTION	99
1.8608-1.9209	0.1924	134	0.1605	2721	X-RAY DIFFRACTION	99
1.9209-1.9895	0.2165	117	0.1573	2692	X-RAY DIFFRACTION	97
1.9895-2.0692	0.2034	127	0.1517	2766	X-RAY DIFFRACTION	100
2.0692-2.1633	0.1731	112	0.1495	2755	X-RAY DIFFRACTION	100
2.1633-2.2774	0.1827	141	0.1501	2723	X-RAY DIFFRACTION	100
2.2774-2.4201	0.1931	138	0.1551	2753	X-RAY DIFFRACTION	99
2.4201-2.6069	0.1836	121	0.1588	2683	X-RAY DIFFRACTION	98
2.6069-2.8693	0.1796	147	0.1621	2726	X-RAY DIFFRACTION	100
2.8693-3.2844	0.1762	158	0.148	2719	X-RAY DIFFRACTION	99
3.2844-4.1377	0.173	151	0.1213	2694	X-RAY DIFFRACTION	97
4.1377-50.289	0.1543	176	0.1343	2715	X-RAY DIFFRACTION	98

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	0.7968	-0.6344	0.4138	0.6309	0.2366	0.9532	0.1518	0.0416	-0.1321	-0.1478	-0.1968	0.0755	0.0482	-0.0383	-0.0325	0.1521	0.018	-0.0064	0.1312	0.0146	0.1313	-17.4008	0.9605	-36.8302
2	0.2696	-0.1722	-0.02	0.061	-0.2424	0.1903	0.0134	0.0772	0.1612	-0.0515	0.0712	0.048	0.1179	-0.0875	0.0039	0.1203	-0.0076	0.0016	0.1171	0.0084	0.119	-19.3019	-1.6292	-25.0996
3	0.169	-0.0179	0.0104	0.2338	0.0994	0.1123	-0.0091	0.1194	-0.0078	-0.0559	-0.0524	-0.1043	0.1102	0.1523	0	0.126	0.0102	0.0203	0.1675	0.0277	0.1231	-1.2231	-3.0741	-32.8935
4	0.1524	-0.1601	0.0204	0.0658	0.0012	0.0901	-0.1252	0.047	0.509	0.1416	0.0909	-0.2272	-0.0603	0.0306	-0.0012	0.1493	-0.0112	-0.0054	0.1321	0.0303	0.1973	-3.4788	7.5734	-27.5503
5	0.2972	0.3942	0.0899	0.603	-0.1422	0.6392	0.028	-0.018	0.0869	0.0081	-0.088	0.1119	-0.1464	-0.0534	-0.0123	0.1374	0.0214	0.0067	0.1085	-0.0199	0.1344	-18.0068	8.2679	-18.0053
6	0.1021	0.2838	-0.2103	0.2058	-0.1643	0.189	0.0135	-0.0058	0.0373	-0.0156	-0.0264	0.0007	0.0884	-0.0489	-0.0001	0.1223	-0.0028	-0.0004	0.1157	0.0119	0.093	-15.9898	-7.5597	-21.7159
7	0.376	-0.032	0.0603	0.1018	-0.1553	0.1152	-0.0107	-0.1698	0.1475	0.125	0.0617	-0.1245	0.0033	0.0193	0.0077	0.1486	-0.0035	-0.0006	0.1246	0.0216	0.1479	-5.1535	-4.5627	-17.8462
8	0.3948	0.1163	-0.3909	0.0229	-0.0515	0.1585	-0.0706	-0.1134	-0.2784	0.0976	-0.1241	-0.2419	0.1512	0.0463	-0.0427	0.1914	0.0045	-0.04	0.1682	0.0443	0.189	-5.0325	-14.5537	-18.5111
9	0.1183	0.0092	0.1131	0.0399	0.0084	0.1225	0.0549	0.006	-0.0632	0.181	-0.0711	0.0492	-0.0015	-0.0349	-0.0001	0.2142	-0.043	-0.0122	0.1583	-0.0144	0.1351	-17.4679	-12.4116	-5.8597
10	0.5029	0.1003	-0.1746	0.1475	-0.2535	0.3415	0.1108	-0.0604	0.0722	0.0858	-0.168	0.1417	0.0003	-0.1912	0.0128	0.1631	-0.0267	0.0301	0.1645	-0.0394	0.1336	-24.3674	-2.8828	-6.8955
11	0.213	-0.2681	0.3157	0.7326	0.3883	0.9751	-0.1712	-0.1235	0.091	0.1814	0.0065	0.0593	-0.2341	-0.0502	-0.0761	0.1494	0.0085	-0.0222	0.135	-0.0368	0.1758	-4.1923	18.8775	12.5067
12	0.5059	0.1464	0.0407	0.7464	0.3371	0.6971	-0.0233	-0.0925	0.0957	0.0744	-0.0714	0.0768	0.0549	0.0267	-0.1836	0.1165	-0.0122	0.0056	0.1343	-0.0288	0.1307	-4.8296	7.6549	8.8734
13	0.4959	0.1157	-0.533	0.2506	0.0344	1.2099	-0.1686	0.0273	0.3327	-0.1469	0.0352	0.6348	0.0195	-0.1496	-0.1999	0.1395	-0.0199	-0.0342	0.184	-0.0347	0.2747	-15.329	7.4835	4.0694
14	1.1416	-0.0541	-0.0004	0.3762	0.3152	0.8099	-0.0964	0.1175	0.2178	-0.0656	0.0489	0.1355	-0.1862	-0.0459	-0.1092	0.1675	-0.0053	-0.059	0.1222	0.0143	0.2064	-6.2033	16.7027	-7.2708
15	0.2916	0.3586	-0.277	0.2361	0.2281	0.2413	-0.0549	-0.0318	0.0246	0.015	0.0547	-0.0664	-0.0177	0.1111	0	0.1134	-0.0023	-0.0099	0.1474	-0.019	0.1391	5.1001	8.517	1.4028
16	0.9781	-0.4851	0.5659	0.304	-0.227	0.5505	0.1245	0.6356	0.2126	-0.0483	-0.2248	0.2245	0.4976	-0.0352	-0.1007	0.185	-0.0422	0.0177	0.1396	-0.0683	0.2092	-4.5976	-1.8693	-0.2653
17	0.2581	0.1245	0.0545	0.0286	-0.0617	0.6107	-0.1577	0.0579	-0.4114	0.2632	0.2933	-0.0357	0.7069	0.6775	0.0295	0.4728	0.1428	-0.017	0.2691	-0.0516	0.3216	8.5175	-4.0667	-1.2169
18	0.0804	0.0028	0.0092	0.2887	0.0697	0.0777	-0.0268	0.4022	-0.0072	-0.1693	0.1194	-0.1834	0.0714	0.5229	-0.016	0.177	-0.0099	0.0258	0.415	-0.1235	0.207	12.222	2.9093	-12.1425
19	0.306	0.1766	-0.3281	0.5971	0.174	0.4103	-0.009	0.3245	0.2877	-0.2264	0.0708	-0.1433	-0.1835	0.3419	0.1742	0.2078	-0.0861	0.0294	0.2948	0.0154	0.1845	8.7908	13.0979	-14.7586

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 33 through 62 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 63 through 76 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 77 through 93 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 94 through 105 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 106 through 138 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 139 through 169 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 170 through 180 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 181 through 197 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 198 through 210 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 211 through 231 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 33 through 62 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 63 through 93 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 94 through 105 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 106 through 138 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 139 through 170 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 171 through 183 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 184 through 199 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 200 through 210 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 211 through 231 )

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