PDB-4gim: Crystal Structure of Pseudouridine Monophosphate Glycosidase Comp...

ID or keywords:

Entry

Database: PDB / ID: 4gim

Title

Crystal Structure of Pseudouridine Monophosphate Glycosidase Complexed with Pseudouridine 5'-phosphate

Components

Pseudouridine-5'-phosphate glycosidase

Keywords

HYDROLASE / alpha-beta-alpha sandwich fold

Function / homology

Function and homology information

nucleobase catabolic process / pseudouridylate synthase / pseudouridylate synthase activity / hydrolase activity, acting on glycosyl bonds / manganese ion binding / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.802 Å

Authors

Huang, S. / Mahanta, N. / Begley, T.P. / Ealick, S.E.

Citation

Journal: Biochemistry / Year: 2012
Title: Pseudouridine monophosphate glycosidase: a new glycosidase mechanism.
Authors: Huang, S. / Mahanta, N. / Begley, T.P. / Ealick, S.E.

History

Deposition	Aug 8, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 31, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 2, 2013	Group: Database references
Revision 1.2	Sep 13, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4gim.cif.gz	198.3 KB	Display	PDBx/mmCIF format
PDB format	pdb4gim.ent.gz	153.5 KB	Display	PDB format
PDBx/mmJSON format	4gim.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4gim_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	4gim_full_validation.pdf.gz	1.3 MB	Display
Data in XML	4gim_validation.xml.gz	39.9 KB	Display
Data in CIF	4gim_validation.cif.gz	58.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gi/4gim ftp://data.pdbj.org/pub/pdb/validation_reports/gi/4gim	HTTPS FTP

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Related structure data

Related structure data	4gijC 4gikC 4gilC 1vkmS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4gij-d 4gik-d 4gil-d 1vkm-1 1dc1-d 3ih8-1 2xqr-6 3eh1-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

Deposited unit

A: Pseudouridine-5'-phosphate glycosidase

B: Pseudouridine-5'-phosphate glycosidase

C: Pseudouridine-5'-phosphate glycosidase

hetero molecules

108 kDa, 3 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)	60.657, 76.511, 199.162
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Pseudouridine-5'-phosphate glycosidase / pseudouridine monophosphate glycosidase / PsiMP glycosidase Mass: 35565.551 Da / Num. of mol.: 3 / Mutation: K166A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: b2165, JW2152, psuG, yeiN / Plasmid: THT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33025, Hydrolases; Glycosylases
#2: Chemical	ChemComp-PSU / PSEUDOURIDINE-5'-MONOPHOSPHATE Type: RNA linking / Mass: 324.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₉H₁₃N₂O₉P
#3: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 643 / 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: 43.11 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG4000, 0.1 M Tris, 0.2 M sodium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

CHESS

/ Beamline: F1 / Wavelength: 0.918 Å

Detector

Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 12, 2011

Radiation

Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.918 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. all: 86553 / Num. obs: 86181 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / R_merge(I) obs: 0.089 / Net I/σ(I): 8.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Diffraction-ID	% possible all
1.8-1.86	4.9	0.565	1	100
1.86-1.94	4.9	0.422	1	100
1.94-2.03	4.9	0.289	1	100
2.03-2.13	4.9	0.205	1	100
2.13-2.27	4.9	0.165	1	100
2.27-2.44	4.9	0.129	1	100
2.44-2.69	4.9	0.101	1	100
2.69-3.08	4.9	0.077	1	100
3.08-3.88	4.9	0.061	1	100
3.88-50	4.7	0.06	1	98.8

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Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.11	data extraction
HKL-2000		data collection
HKL-2000		data reduction
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VKM

1vkm

Resolution: 1.802→35.331 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / σ(F): 1.35 / Phase error: 20.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2072	4311	5 %
R_work	0.1772	-	-
obs	0.1787	86169	99.6 %
all	-	86553	-

Solvent computation

Shrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 41.255 Å² / k_sol: 0.361 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	9.7156 Å²	-0 Å²	-0 Å²
2-	-	-5.4306 Å²	0 Å²
3-	-	-	-4.285 Å²

Refinement step

Cycle: LAST / Resolution: 1.802→35.331 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6574	0	66	643	7283

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	6760
X-RAY DIFFRACTION	f_angle_d	1.222	9221
X-RAY DIFFRACTION	f_dihedral_angle_d	14.526	2415
X-RAY DIFFRACTION	f_chiral_restr	0.08	1146
X-RAY DIFFRACTION	f_plane_restr	0.006	1187

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 (%)
1.8021-1.8226	0.2953	151	0.2917	2511	X-RAY DIFFRACTION	93
1.8226-1.8441	0.3748	115	0.2888	2767	X-RAY DIFFRACTION	100
1.8441-1.8666	0.2899	145	0.2403	2670	X-RAY DIFFRACTION	100
1.8666-1.8902	0.2804	140	0.2347	2699	X-RAY DIFFRACTION	100
1.8902-1.9151	0.2708	135	0.2257	2744	X-RAY DIFFRACTION	100
1.9151-1.9413	0.2829	146	0.2095	2656	X-RAY DIFFRACTION	100
1.9413-1.969	0.2451	144	0.2017	2684	X-RAY DIFFRACTION	100
1.969-1.9984	0.2269	163	0.1825	2712	X-RAY DIFFRACTION	100
1.9984-2.0296	0.1984	119	0.1741	2736	X-RAY DIFFRACTION	100
2.0296-2.0629	0.2069	130	0.1671	2699	X-RAY DIFFRACTION	100
2.0629-2.0985	0.1952	141	0.17	2714	X-RAY DIFFRACTION	100
2.0985-2.1366	0.2011	135	0.1693	2741	X-RAY DIFFRACTION	100
2.1366-2.1777	0.2121	145	0.1695	2701	X-RAY DIFFRACTION	100
2.1777-2.2222	0.2083	137	0.1709	2716	X-RAY DIFFRACTION	100
2.2222-2.2705	0.2179	140	0.1711	2730	X-RAY DIFFRACTION	100
2.2705-2.3233	0.2216	138	0.1631	2725	X-RAY DIFFRACTION	100
2.3233-2.3814	0.194	151	0.1631	2701	X-RAY DIFFRACTION	100
2.3814-2.4457	0.1932	139	0.1711	2729	X-RAY DIFFRACTION	100
2.4457-2.5177	0.1939	140	0.1756	2736	X-RAY DIFFRACTION	100
2.5177-2.5989	0.2059	145	0.1767	2714	X-RAY DIFFRACTION	100
2.5989-2.6918	0.2053	155	0.1714	2714	X-RAY DIFFRACTION	100
2.6918-2.7995	0.2367	158	0.1838	2735	X-RAY DIFFRACTION	100
2.7995-2.9269	0.22	173	0.1824	2736	X-RAY DIFFRACTION	100
2.9269-3.0811	0.1988	164	0.1837	2714	X-RAY DIFFRACTION	100
3.0811-3.274	0.193	146	0.1837	2761	X-RAY DIFFRACTION	100
3.274-3.5266	0.199	159	0.1749	2763	X-RAY DIFFRACTION	100
3.5266-3.8811	0.1868	122	0.1622	2811	X-RAY DIFFRACTION	100
3.8811-4.4417	0.1643	147	0.1446	2802	X-RAY DIFFRACTION	100
4.4417-5.5925	0.1737	144	0.1493	2837	X-RAY DIFFRACTION	100
5.5925-35.3379	0.2319	144	0.205	2900	X-RAY DIFFRACTION	97

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	1.8362	-1.1037	-1.7169	0.655	1.008	1.5941	-0.1631	0.0166	0.2609	0.0071	0.3061	-1.1058	-0.695	0.7851	-0.0466	0.0315	-0.3088	0.0738	0.4631	-0.1652	0.6346	31.5886	-7.3904	-17.1816
2	2.373	0.305	0.483	0.9953	0.2879	2.8359	-0.0559	0.0132	0.2315	-0.1473	0.0925	-0.198	-0.6547	0.1913	-0.0778	0.2993	-0.093	0.0221	0.1581	-0.0327	0.2371	15.3389	2.2044	-15.7428
3	1.2831	0.5904	-0.2027	1.2739	0.4088	1.6727	-0.1637	0.1374	0.1854	-0.5507	0.2448	-0.2729	-0.6622	0.344	-0.1133	0.3831	-0.139	0.0969	0.2284	-0.0528	0.2727	20.2613	-3.2706	-25.7098
4	0.5034	-0.1356	0.185	1.3601	0.3517	1.7717	-0.0479	0.0348	0.0094	-0.1867	0.1034	-0.1019	-0.1691	0.0901	-0.0468	0.0895	-0.0304	0.0035	0.116	-0.0194	0.1278	9.4293	-15.8348	-17.9843
5	1.761	-0.5735	-0.4262	1.6074	0.3187	1.6935	-0.079	-0.1171	-0.0736	0.1239	0.1256	-0.1924	0.0271	0.1509	-0.0469	0.0708	-0.0124	-0.0115	0.1449	-0.0199	0.152	12.8608	-20.9431	-4.9534
6	4.5624	-4.9404	-1.5953	7.5199	2.3188	2.3218	-0.1042	-0.0347	-0.0128	0.1575	0.1598	-0.0449	-0.104	0.0478	-0.0628	0.0609	-0.0444	0.0031	0.1305	-0.0251	0.1485	9.1252	-12.42	-7.6169
7	3.2125	0.0264	0.4815	3.8738	-0.475	2.0045	-0.0625	-0.076	0.1386	-0.0895	0.1194	0.3171	-0.0355	-0.6095	-0.0487	0.1781	0.0415	-0.028	0.2062	0.0215	0.2027	-8.5424	-5.044	-19.5772
8	1.2629	-0.6232	-1.2992	1.6018	1.8748	5.182	0.0286	0.0953	0.1352	-0.3044	0.0387	0.1158	-0.41	-0.2401	-0.0504	0.2574	0.0002	-0.056	0.1618	0.0323	0.2098	-0.9189	-2.013	-23.749
9	4.1646	-2.0977	2.1626	1.9456	-1.3826	2.3718	-0.0814	-0.1617	0.2155	0.0441	0.0722	-0.2421	-0.1575	0.1206	0.0289	0.115	-0.028	-0.0177	0.1359	-0.0354	0.1521	15.9844	-7.3868	-6.5161
10	2.2537	1.1679	0.4237	0.7099	-0.0231	0.8044	0.2326	0.179	-0.5411	0.2207	0.1839	-0.5954	0.7459	0.7096	-0.3207	0.4041	0.1826	-0.171	0.331	-0.1569	0.4227	26.471	-46.6309	-10.0289
11	1.0357	-0.2407	0.3462	2.7648	0.963	0.7693	0.1281	-0.2646	-0.4088	0.6689	0.0403	0.2668	0.973	-0.1505	-0.139	0.676	-0.0535	-0.1258	0.1627	0.0354	0.3343	8.5558	-52.4167	-6.3193
12	1.3539	-0.5708	0.2946	3.0963	1.1201	2.3009	0.0125	-0.1525	-0.1662	0.5254	0.133	-0.158	0.5144	0.0981	-0.13	0.228	0.0176	-0.0622	0.1451	-0.0161	0.1946	14.7366	-40.1273	-5.8764
13	0.5701	0.0433	0.411	1.9053	0.4618	1.9368	0.0707	0.1021	-0.2181	-0.0617	0.0561	0.0658	0.4406	-0.0323	-0.1245	0.2185	-0.0256	-0.0503	0.1329	-0.0321	0.1866	6.1424	-44.5611	-25.2963
14	1.2028	0.8566	0.2866	0.6152	0.2312	0.3007	-0.0154	-0.0703	-0.1662	-0.112	0.1118	0.6462	0.1635	-0.5856	0.0106	0.1596	-0.1578	-0.0182	0.3553	0.0504	0.4844	-12.2629	-40.0834	-13.6624
15	3.012	1.7901	-0.4016	4.6323	-0.6774	1.2174	0.2202	-0.1417	-0.1414	0.5292	-0.1206	0.4986	0.2959	-0.3757	-0.0745	0.2195	-0.1065	0.0069	0.2297	0.0285	0.2477	-6.4766	-42.1573	-8.389
16	3.2161	-0.6058	-0.97	1.9171	0.3977	2.4895	0.2982	-0.071	-0.3904	0.0767	-0.0692	-0.046	0.7443	0.2395	-0.2179	0.4659	0.0113	-0.119	0.1459	-0.0397	0.2758	10.2665	-55.4944	-17.984
17	0.9278	-0.2806	0.0284	1.8761	-0.4392	2.3118	0.1303	0.2511	0.0053	-0.594	0.1274	-0.4479	-0.1943	0.6993	-0.2104	0.4757	-0.0527	0.1222	0.4093	-0.1359	0.2854	20.7266	-33.481	-54.295
18	0.7299	-0.2755	-0.0857	1.7183	0.6649	1.8186	0.0912	0.1677	-0.0525	-0.5882	0.0634	-0.1033	-0.1885	0.2264	-0.1455	0.3197	-0.0491	0.0217	0.2024	-0.0474	0.1521	12.0744	-30.737	-43.6259
19	0.8518	-0.1103	0.249	1.3955	1.0712	1.6846	0.0201	0.167	0.0491	-0.8422	0.08	-0.0294	-0.84	0.0224	-0.101	0.6333	-0.0501	0.0417	0.2347	0.0465	0.1748	7.4097	-18.8229	-46.7739
20	1.4457	-0.0956	-0.0899	1.3127	0.1567	1.9875	0.1665	0.1988	0.082	-0.7952	-0.0046	0.118	-0.5946	0.1359	-0.1216	0.6089	-0.0377	0.0388	0.2138	-0.0356	0.122	8.1398	-27.3131	-52.8372

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 6:30)
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 31:57)
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 58:104)
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 105:198)
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 199:224)
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 225:244)
7	X-RAY DIFFRACTION	7	chain 'A' and (resseq 245:262)
8	X-RAY DIFFRACTION	8	chain 'A' and (resseq 263:283)
9	X-RAY DIFFRACTION	9	chain 'A' and (resseq 284:311)
10	X-RAY DIFFRACTION	10	chain 'B' and (resseq 5:30)
11	X-RAY DIFFRACTION	11	chain 'B' and (resseq 31:58)
12	X-RAY DIFFRACTION	12	chain 'B' and (resseq 59:123)
13	X-RAY DIFFRACTION	13	chain 'B' and (resseq 124:244)
14	X-RAY DIFFRACTION	14	chain 'B' and (resseq 245:265)
15	X-RAY DIFFRACTION	15	chain 'B' and (resseq 266:283)
16	X-RAY DIFFRACTION	16	chain 'B' and (resseq 284:310)
17	X-RAY DIFFRACTION	17	chain 'C' and (resseq 6:58)
18	X-RAY DIFFRACTION	18	chain 'C' and (resseq 59:198)
19	X-RAY DIFFRACTION	19	chain 'C' and (resseq 199:262)
20	X-RAY DIFFRACTION	20	chain 'C' and (resseq 263:310)

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-Basic information

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-Download

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

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Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

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Validation report

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Related structure data

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Links

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Assembly

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Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

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Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi