PDB-3q91: Crystal Structure of Human Uridine Diphosphate Glucose Pyrophosph...

ID or keywords:

Entry

Database: PDB / ID: 3q91

Title

Crystal Structure of Human Uridine Diphosphate Glucose Pyrophosphatase (NUDT14)

Components

Uridine diphosphate glucose pyrophosphatase

Keywords

HYDROLASE / Structural Genomics / Structural Genomics Consortium / SGC / NUDIX / MutT-like / Magnesium Binding

Function / homology

Function and homology information

Synthesis of dolichyl-phosphate-glucose / UDP-sugar diphosphatase / UDP-sugar diphosphatase activity / protein N-linked glycosylation via asparagine / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / identical protein binding / metal ion binding / cytosol
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.7 Å

Authors

Tresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. ...

Citation

Journal: To be Published
Title: Crystal Structure of Human Uridine Diphosphate Glucose Pyrophosphatase (NUDT14)
Authors: Tresaugues, L. / Siponen, M.I. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Ekblad, T. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / ...

History

Deposition	Jan 7, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 13, 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 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3q91.cif.gz	240.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3q91.ent.gz	195.3 KB	Display	PDB format
PDBx/mmJSON format	3q91.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3q91_validation.pdf.gz	460.3 KB	Display	wwPDB validaton report
Full document	3q91_full_validation.pdf.gz	466.5 KB	Display
Data in XML	3q91_validation.xml.gz	21.2 KB	Display
Data in CIF	3q91_validation.cif.gz	28.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/q9/3q91 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/3q91	HTTPS FTP

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Related structure data

Related structure data	1g0sS 1viqS 1viuS 2dsbS 3q90 3q93 S: Starting model for refinement
Similar structure data	6g77-1 5ylc-d 4li3-d 4k4a-1 5lih-1 3lvp-4 4jxg-1 2i0y-d 1y7l-d 4y73-4 Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#145 - Jan 2012 Messenger RNA Capping similarity (3) #201 - Sep 2016 Isoprene Synthase similarity (3)

Deposited unit

A: Uridine diphosphate glucose pyrophosphatase

C: Uridine diphosphate glucose pyrophosphatase

B: Uridine diphosphate glucose pyrophosphatase

D: Uridine diphosphate glucose pyrophosphatase

95.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uridine diphosphate glucose pyrophosphatase

B: Uridine diphosphate glucose pyrophosphatase

defined by author&software
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Uridine diphosphate glucose pyrophosphatase

D: Uridine diphosphate glucose pyrophosphatase

defined by author&software
47.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	84.040, 106.240, 106.350
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#1: Protein	Uridine diphosphate glucose pyrophosphatase / UDPG pyrophosphatase / UGPPase / Nucleoside diphosphate-linked moiety X motif 14 / Nudix motif 14 Mass: 23768.596 Da / Num. of mol.: 4 / Fragment: unp residues 28-222 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT14, UGPP / Plasmid: pNIC-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE / References: UniProt: O95848, UDP-sugar diphosphatase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Uridine diphosphate glucose pyrophosphatase / UDPG pyrophosphatase / UGPPase / Nucleoside diphosphate-linked moiety X motif 14 / Nudix motif 14

Mass: 23768.596 Da / Num. of mol.: 4 / Fragment: unp residues 28-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: NUDT14, UGPP / Plasmid: pNIC-BSA4 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) R3 pRARE / References: UniProt: O95848, UDP-sugar diphosphatase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.5 Å³/Da / Density % sol: 50.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 % w/v PEG3350, 0.2 M AMMONIUM FORMATE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
Detector	Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 2, 2009 / Details: MIRRORS
Radiation	Monochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.91841 Å / Relative weight: 1
Reflection	Resolution: 2.7→53.17 Å / Num. all: 26804 / Num. obs: 26724 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / B_iso Wilson estimate: 83.8 Å² / R_merge(I) obs: 0.063 / R_sym value: 0.063 / Net I/σ(I): 8.5
Reflection shell	Resolution: 2.7→2.85 Å / Redundancy: 4.8 % / R_merge(I) obs: 0.708 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3827 / R_sym value: 0.708 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
PHASER		phasing
REFMAC	5.5.0102	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 1G0S, 1VIQ, 1VIU and 2DSB

Resolution: 2.7→53.17 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.912 / SU B: 31.316 / SU ML: 0.279 / Cross valid method: THROUGHOUT / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27137	1376	5.2 %	RANDOM
R_work	0.22844	-	-	-
obs	0.23054	25328	99.53 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 68.955 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	4.87 Å²	0 Å²	0 Å²
2-	-	-2.13 Å²	0 Å²
3-	-	-	-2.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.7→53.17 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4399	0	0	5	4404

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.022	4485
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2950
X-RAY DIFFRACTION	r_angle_refined_deg	1.068	1.958	6100
X-RAY DIFFRACTION	r_angle_other_deg	0.767	3	7177
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.158	5	555
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.676	23.869	199
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.718	15	698
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.61	15	30
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	708
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	4964
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	906
X-RAY DIFFRACTION	r_mcbond_it	0.322	1.5	2825
X-RAY DIFFRACTION	r_mcbond_other	0.048	1.5	1152
X-RAY DIFFRACTION	r_mcangle_it	0.628	2	4541
X-RAY DIFFRACTION	r_scbond_it	0.84	3	1660
X-RAY DIFFRACTION	r_scangle_it	1.438	4.5	1559

LS refinement shell

Resolution: 2.7→2.77 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.429	103	-
R_work	0.391	1837	-
obs	-	1837	99.18 %

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	17.5115	2.7398	-0.2046	0.6904	-1.3606	6.9492	1.2168	-1.0648	0.1771	0.2239	-0.1294	0.2746	0.0274	-0.0844	-1.0875	0.6356	0.0391	0.1796	0.6773	-0.0244	0.378	-7.0004	22.344	23.4115
2	26.7879	-5.2382	8.3266	23.3049	-6.5826	5.2526	-0.6187	1.9844	0.0085	-1.9754	0.2215	0.866	-0.6551	0.353	0.3972	1.1489	0.0884	-0.0795	1.0466	0.1877	0.8286	-19.1082	32.6584	7.0328
3	22.4858	2.1726	8.1192	6.9037	4.3576	6.8414	-0.8261	-0.6004	2.0329	1.149	-0.2352	1.2324	-0.3884	0.1635	1.0614	0.7642	-0.1121	0.1735	0.6956	-0.0376	0.3931	-5.0054	32.0383	25.8208
4	10.0074	2.1046	-4.4373	7.0356	-2.0285	9.7658	0.1566	-0.5712	-0.125	-0.005	-0.0202	0.0864	0.1469	0.4778	-0.1365	0.478	-0.0103	-0.0913	0.6674	-0.0478	0.1412	-2.0161	24.9353	27.8674
5	5.5208	5.5513	1.9662	5.7541	0.8441	10.6975	-0.2221	0.2741	-0.1491	-0.3327	0.3236	-0.0204	-0.0359	-0.7103	-0.1015	0.6179	0.041	-0.1166	0.7182	0.0023	0.4703	-11.5887	19.1592	15.0597
6	21.1482	-17.1583	3.5359	18.6117	-9.8546	12.7233	-0.4416	-1.4158	-0.8656	-0.9478	0.857	-0.0526	1.8986	0.5218	-0.4154	0.7686	0.0086	0.1741	0.5166	-0.1876	1.2769	1.4587	14.1766	17.6917
7	23.1552	-4.0998	-2.2699	10.3743	0.1816	8.6445	0.2035	0.4908	-0.1454	-0.2377	-0.0088	-0.7458	-0.3494	0.445	-0.1947	0.5417	-0.0924	-0.0048	0.6444	-0.0561	0.1535	8.5592	26.2575	-0.7259
8	185.8083	-7.1007	-22.0832	148.1092	79.0164	43.9756	-0.5953	-16.2901	15.9112	10.8672	-1.1341	6.372	5.9106	1.0403	1.7295	1.6467	-0.2951	0.4746	2.9371	-1.3404	1.9187	8.8395	42.8453	9.9849
9	12.7001	5.5851	3.0359	12.9029	-1.193	1.3763	-0.0663	0.6166	2.3508	-0.7005	-0.542	0.7831	0.0252	0.1969	0.6083	0.8038	0.1249	0.1589	1.0476	0.0617	0.4807	-0.1272	34.502	-1.0084
10	7.3725	0.3576	-5.6988	3.9391	-2.3533	12.4104	0.3809	0.1115	0.1114	0.0399	-0.0441	0.0819	-0.1118	-0.2986	-0.3368	0.6171	-0.0728	-0.0489	0.7281	0.0004	0.155	-0.1826	28.277	-2.8224
11	5.7141	0.4581	2.4103	0.0582	-0.0216	7.5678	0.3036	-0.0718	0.2717	0.0281	-0.0133	-0.0451	-0.071	0.8721	-0.2903	0.725	0.0018	-0.0189	0.7596	-0.1112	0.4983	13.368	26.2716	1.7192
12	7.6817	0.9563	-3.8081	6.6524	-1.1761	6.7072	-0.157	-0.2937	-0.8133	0.256	0.1032	-0.5856	0.9849	0.618	0.0538	0.4815	0.0148	-0.1008	0.7205	-0.0342	0.3154	8.5888	20.7027	7.9642
13	10.2401	1.4028	-1.7918	5.6405	-1.243	3.914	0.3896	0.3052	0.5176	0.2171	-0.3479	-0.6051	-0.3021	1.2962	-0.0417	0.6257	-0.047	0.0427	0.5197	-0.0119	0.8682	52.8731	32.1877	25.7977
14	8.8962	1.8467	-4.1266	7.0588	-0.9243	6.5653	-0.3534	1.0116	-0.547	-1.0432	0.2837	-0.0881	1.2135	0.2193	0.0697	0.4583	0.0504	-0.0634	0.3251	0.037	0.7984	45.5201	24.5971	20.2248
15	12.8244	-2.9205	2.152	6.6266	1.9493	2.0441	-0.2475	-0.4208	-0.0795	-0.0418	-0.0484	0.0883	0.0865	0.1686	0.2959	0.6422	-0.017	0.0036	0.2014	0.042	0.7311	46.4514	18.3177	27.5745
16	10.1304	-0.5583	6.3233	13.642	-4.6999	31.2437	-0.0922	0.7419	-0.0191	-0.9906	0.0841	0.6194	-0.2806	-0.6164	0.0081	0.3646	0.0243	0.0343	0.2827	-0.0741	0.7369	37.2079	31.0132	22.7633
17	3.7528	1.5908	0.2911	7.3926	1.91	1.744	0.1084	-0.0308	0.0432	0.9726	-0.3327	-0.713	0.0029	0.3137	0.2243	0.7105	0.0098	-0.1223	0.4408	0.0784	0.8486	53.9157	28.4852	33.7741
18	10.2952	-0.3247	-0.8955	3.538	0.5247	6.4035	-0.2659	-0.9501	-0.1262	1.1072	0.0809	-0.3477	0.1809	0.1591	0.1851	0.7931	0.0096	-0.0305	0.3035	-0.0498	0.5882	45.1202	34.643	36.0694
19	29.1497	-8.4191	22.5338	2.4355	-6.5115	17.4572	-1.0626	2.4492	1.4442	0.2974	-0.5099	-0.4572	-1.0144	1.8992	1.5725	1.4791	-0.0801	0.0281	0.2074	0.1689	1.9011	43.3277	50.1061	21.3951
20	2.6286	3.1658	2.2409	14.2713	13.5822	14.8984	0.0934	0.2718	0.0603	-0.0044	0.0775	0.208	-0.1096	-0.4269	-0.1709	0.6006	0.0762	0.0442	0.4562	0.1221	0.7452	28.5491	42.7593	20.7352
21	10.426	-3.1979	1.6595	10.1859	-0.1969	2.5975	-0.0285	0.5358	0.475	-0.3461	-0.1283	-0.3653	-0.6165	0.1744	0.1568	0.7298	-0.0585	0.0615	0.2102	-0.0156	0.7548	41.8982	55.5357	23.6428
22	19.2069	-8.9952	-13.9715	20.0553	18.2257	29.2979	0.2252	1.2276	-1.1196	-0.5394	-0.481	-0.3853	0.1391	0.3333	0.2558	0.665	0.1051	-0.0447	0.3477	0.0437	0.8058	46.4089	45.8642	23.0358
23	3.1275	1.9328	-1.1406	9.2032	1.5421	1.828	0.0223	-0.0454	-0.0053	0.4705	-0.2928	0.9891	-0.0148	-0.5343	0.2705	0.5591	-0.0016	0.0512	0.432	-0.02	0.8042	28.1875	45.8873	28.0198
24	8.1374	-5.2053	-3.987	3.7125	1.0345	19.6758	-1.2101	-1.2984	-1.0281	1.0792	0.3618	1.0056	-2.6374	1.4335	0.8482	0.8104	0.0137	0.1622	0.924	-0.2999	0.88	35.9126	44.4904	37.3689

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	39 - 61
2	X-RAY DIFFRACTION	2	A	62 - 72
3	X-RAY DIFFRACTION	3	A	97 - 117
4	X-RAY DIFFRACTION	4	A	118 - 176
5	X-RAY DIFFRACTION	5	A	177 - 202
6	X-RAY DIFFRACTION	6	A	203 - 220
7	X-RAY DIFFRACTION	7	B	40 - 58
8	X-RAY DIFFRACTION	8	B	59 - 66
9	X-RAY DIFFRACTION	9	B	97 - 116
10	X-RAY DIFFRACTION	10	B	117 - 155
11	X-RAY DIFFRACTION	11	B	156 - 196
12	X-RAY DIFFRACTION	12	B	197 - 220
13	X-RAY DIFFRACTION	13	C	40 - 72
14	X-RAY DIFFRACTION	14	C	97 - 117
15	X-RAY DIFFRACTION	15	C	118 - 137
16	X-RAY DIFFRACTION	16	C	138 - 157
17	X-RAY DIFFRACTION	17	C	158 - 196
18	X-RAY DIFFRACTION	18	C	197 - 220
19	X-RAY DIFFRACTION	19	D	39 - 47
20	X-RAY DIFFRACTION	20	D	48 - 102
21	X-RAY DIFFRACTION	21	D	103 - 143
22	X-RAY DIFFRACTION	22	D	144 - 157
23	X-RAY DIFFRACTION	23	D	158 - 202
24	X-RAY DIFFRACTION	24	D	203 - 220

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