PDB-11wx: Crystal Structure of ribosomal large subunit pseudouridine syntha...

ID or keywords:

Entry

Database: PDB / ID: 11wx

Title

Crystal Structure of ribosomal large subunit pseudouridine synthase D from Neisseria gonorrhoea

Components

Pseudouridine synthase

Keywords

LYASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Pseudouridine synthase / Neisseria gonorrhoeas

Function / homology

Function and homology information

23S rRNA pseudouridine(1911/1915/1917) synthase activity / enzyme-directed rRNA pseudouridine synthesis / Isomerases; Intramolecular transferases; Transferring other groups / RNA binding / cytoplasm
Similarity search - Function

Biological species

Neisseria gonorrhoeae NCCP11945 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.91 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	75N93022C00036	United States
National Institutes of Health/Office of the Director	S10OD030394	United States

Citation

Journal: To be published
Title: Crystal Structure of ribosomal large subunit pseudouridine synthase D from Neisseria gonorrhoea
Authors: Ung, A.R. / Lovell, S. / Battaile, K.P.

History

Deposition	Mar 16, 2026	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 25, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	11wx.cif.gz	307.6 KB	Display	PDBx/mmCIF format
PDB format	pdb11wx.ent.gz		Display	PDB format
PDBx/mmJSON format	11wx.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/1w/11wx ftp://data.pdbj.org/pub/pdb/validation_reports/1w/11wx	HTTPS FTP

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Related structure data

Similar structure data	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 synthase

B: Pseudouridine synthase

C: Pseudouridine synthase

hetero molecules

84.6 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pseudouridine synthase

hetero molecules

defined by author
Evidence: gel filtration, monomeric
28.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Pseudouridine synthase

hetero molecules

defined by author
28.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: Pseudouridine synthase

hetero molecules

defined by author
28.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	132.552, 88.011, 101.659
Angle α, β, γ (deg.)	90.00, 95.18, 90.00
Int Tables number	5
Space group name H-M	C121

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Protein , 1 types, 3 molecules ABC

#1: Protein	Pseudouridine synthase Mass: 27928.064 Da / Num. of mol.: 3 / Fragment: L96-S340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neisseria gonorrhoeae NCCP11945 (bacteria) Gene: NGK_0423 / Plasmid: NegoA.19228.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B4RJW3, Isomerases; Intramolecular transferases; Transferring other groups

#1: Protein

Pseudouridine synthase

Mass: 27928.064 Da / Num. of mol.: 3 / Fragment: L96-S340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Neisseria gonorrhoeae NCCP11945 (bacteria)
Gene: NGK_0423 / Plasmid: NegoA.19228.a.B2 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B4RJW3, Isomerases; Intramolecular transferases; Transferring other groups

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Non-polymers , 5 types, 490 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.52 Å³/Da / Density % sol: 65.1 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Index B12L 2.8 M Sodium acetate. NegoA.19228.a.B2.PW39479 at 18.4 mg/mL. 5 mM Uridine 5'-monophosphate disodium salt (UMP) added prior to crystallization but no electron density was observed ...Details: Index B12L 2.8 M Sodium acetate. NegoA.19228.a.B2.PW39479 at 18.4 mg/mL. 5 mM Uridine 5'-monophosphate disodium salt (UMP) added prior to crystallization but no electron density was observed for these. plate 20669 B12 drop 2, Puck: PSL-0811, Cryo: 75% crystallant + 25% glycerol

Crystal

Density Matthews: 3.52 Å³/Da / Density % sol: 65.1 %

Crystal grow

Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Index B12L 2.8 M Sodium acetate. NegoA.19228.a.B2.PW39479 at 18.4 mg/mL. 5 mM Uridine 5'-monophosphate disodium salt (UMP) added prior to crystallization but no electron density was observed ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
Detector	Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Feb 6, 2026
Radiation	Monochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9786 Å / Relative weight: 1
Reflection	Resolution: 1.91→44.01 Å / Num. obs: 89815 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC_1/2: 1 / R_merge(I) obs: 0.055 / R_pim(I) all: 0.023 / R_rim(I) all: 0.06 / Χ²: 1.01 / Net I/σ(I): 18 / Num. measured all: 620626
Reflection shell	Resolution: 1.91→1.94 Å / % possible obs: 99.2 % / Redundancy: 7.1 % / R_merge(I) obs: 1.368 / Num. measured all: 32287 / Num. unique obs: 4577 / CC_1/2: 0.802 / R_pim(I) all: 0.551 / R_rim(I) all: 1.477 / Χ²: 1.04 / Net I/σ(I) obs: 1.6

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Processing

Software

Name	Version	Classification
PHENIX	2.0_5936	refinement
Aimless		data scaling
XDS		data reduction
PHASER		phasing
PDB_EXTRACT		data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.91→44.01 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1931	4549	5.07 %
R_work	0.1679	-	-
obs	0.1692	89675	99.42 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.91→44.01 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5656	0	37	471	6164

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5807
X-RAY DIFFRACTION	f_angle_d	1.002	7905
X-RAY DIFFRACTION	f_dihedral_angle_d	15.198	2132
X-RAY DIFFRACTION	f_chiral_restr	0.062	905
X-RAY DIFFRACTION	f_plane_restr	0.012	1034

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 (%)
1.91-1.93	0.3357	149	0.3257	2780	X-RAY DIFFRACTION	99
1.93-1.95	0.3266	149	0.2941	2842	X-RAY DIFFRACTION	99
1.95-1.98	0.2975	141	0.2586	2813	X-RAY DIFFRACTION	99
1.98-2	0.3056	153	0.2482	2813	X-RAY DIFFRACTION	99
2-2.03	0.2125	152	0.2205	2807	X-RAY DIFFRACTION	99
2.03-2.06	0.2886	136	0.2092	2809	X-RAY DIFFRACTION	99
2.06-2.09	0.2332	169	0.2113	2805	X-RAY DIFFRACTION	99
2.09-2.12	0.2192	165	0.2038	2809	X-RAY DIFFRACTION	99
2.12-2.15	0.2379	155	0.1971	2860	X-RAY DIFFRACTION	99
2.15-2.19	0.2345	129	0.1989	2788	X-RAY DIFFRACTION	99
2.19-2.22	0.2407	138	0.2022	2851	X-RAY DIFFRACTION	99
2.22-2.26	0.2228	159	0.1953	2836	X-RAY DIFFRACTION	99
2.26-2.31	0.229	158	0.1816	2829	X-RAY DIFFRACTION	100
2.31-2.36	0.1838	135	0.1801	2819	X-RAY DIFFRACTION	99
2.36-2.41	0.1905	158	0.1657	2828	X-RAY DIFFRACTION	99
2.41-2.46	0.2075	166	0.1664	2824	X-RAY DIFFRACTION	99
2.46-2.52	0.1966	162	0.1639	2807	X-RAY DIFFRACTION	99
2.52-2.59	0.1934	177	0.1638	2827	X-RAY DIFFRACTION	100
2.59-2.67	0.1989	147	0.1644	2853	X-RAY DIFFRACTION	100
2.67-2.75	0.2129	146	0.176	2863	X-RAY DIFFRACTION	100
2.75-2.85	0.2333	166	0.1894	2807	X-RAY DIFFRACTION	100
2.85-2.97	0.2079	132	0.1925	2855	X-RAY DIFFRACTION	100
2.97-3.1	0.1993	153	0.1766	2851	X-RAY DIFFRACTION	100
3.1-3.27	0.2036	168	0.1713	2845	X-RAY DIFFRACTION	100
3.27-3.47	0.1941	156	0.1564	2853	X-RAY DIFFRACTION	100
3.47-3.74	0.1716	167	0.148	2834	X-RAY DIFFRACTION	100
3.74-4.11	0.1482	159	0.1334	2849	X-RAY DIFFRACTION	99
4.11-4.71	0.136	133	0.1217	2889	X-RAY DIFFRACTION	99
4.71-5.93	0.1585	132	0.1507	2919	X-RAY DIFFRACTION	100
5.93-44.01	0.2134	139	0.1881	2961	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	1.7385	0.2606	-1.1443	1.5449	-1.5662	3.1092	0.1088	-0.3599	-0.1712	0.0607	-0.2376	-0.1964	0.2522	0.8222	0.1083	0.4473	0.0761	0.009	0.5213	-0.0071	0.4556	49.9146	-9.11	37.4119
2	5.8384	3.1028	-0.3177	5.0067	-1.598	3.4861	0.0939	-0.3122	-0.61	0.0662	-0.5205	-0.5146	0.5016	0.7133	0.3868	0.4343	0.1441	0.0243	0.5202	0.1365	0.4834	51.562	-11.8634	38.5345
3	6.3867	0.6187	-0.1172	0.8585	-0.2649	2.3441	0.0877	-0.4633	0.2198	0.2333	-0.1906	-0.0874	-0.1501	0.4369	0.0998	0.3475	0.0084	-0.0038	0.4312	-0.0163	0.2865	46.7758	3.0161	35.0668
4	1.2546	-0.2651	-0.3173	4.4792	-4.6176	6.28	0.0804	-0.1658	0.0557	0.6017	-0.085	-0.1114	-0.5722	0.176	0.051	0.3959	0.0455	0.0115	0.3001	-0.0356	0.2971	30.4355	9.3013	44.2697
5	1.6543	0.2421	-0.1773	2.3324	0.2806	4.0511	0.0118	0.0502	-0.1258	0.066	-0.0586	-0.153	0.006	0.1257	0.0364	0.2722	0.026	0.0015	0.2816	0.0059	0.3302	30.8854	8.6616	33.9524
6	3.1207	-0.8133	2.4306	4.3286	0.7336	2.6939	0.0995	0.0824	-0.3071	-0.2477	-0.0067	0.5185	0.1848	-0.768	-0.0521	0.3325	-0.0547	-0.0084	0.4743	0.0105	0.472	18.6207	-1.2509	29.5136
7	5.6825	0.6356	0.2762	1.3362	0.0064	2.4557	-0.0206	0.4404	-0.0459	-0.1506	-0.0436	-0.0539	-0.0155	0.1086	0.0758	0.301	0.0429	0.0193	0.2707	-0.033	0.2841	37.1772	2.8968	23.4689
8	2.9167	-1.1037	-2.279	2.4915	1.1429	4.6009	-0.3101	0.2752	-0.1688	0.0553	-0.0684	0.3194	0.4868	-0.716	0.3745	0.4258	-0.0552	-0.007	0.488	-0.0464	0.3528	29.7236	-2.8789	1.8837
9	2.9315	0.5223	-0.0644	4.3085	-0.0023	2.9853	-0.1373	-0.2698	-0.2353	0.8775	-0.1106	0.0861	0.9548	-0.0931	0.2197	0.669	0.0024	0.0824	0.3777	0.0096	0.2713	39.6245	-7.6667	3.9495
10	4.0044	3.7299	-2.562	3.4343	-2.2758	2.3543	-0.1214	-0.0992	-0.233	0.2811	-0.0582	-0.2249	0.5077	0.0785	0.2429	0.5601	0.064	-0.0584	0.2973	-0.0017	0.2921	51.037	-2.0349	-0.6233
11	3.4093	-0.4495	-3.7574	1.8192	0.8223	7.0987	-0.0914	-0.4673	-0.256	0.3435	-0.0503	0.1187	-0.0314	0.2762	0.1329	0.381	0.0013	0.0073	0.4368	0.0012	0.3323	56.4148	7.1131	11.686
12	2.042	-1.2522	0.9724	3.1127	-0.4467	5.8569	-0.1252	0.125	-0.1314	-0.0566	0.1875	0.2717	0.1654	-0.0702	-0.0488	0.3761	-0.0181	0.0403	0.2947	-0.0301	0.3693	57.4004	5.3567	-3.2635
13	7.6332	0.4943	-1.5732	1.4725	-1.8057	5.8516	0.0008	-0.3491	0.0084	0.0614	-0.1318	-0.0741	-0.0922	-0.0528	0.1111	0.3803	-0.0065	0.0185	0.249	-0.0383	0.2774	53.1057	8.2715	6.0817
14	5.8615	1.7394	-2.3466	5.1229	-3.6887	6.7573	0.0465	0.3457	0.7704	-0.2871	-0.1468	-0.0564	-1.1133	0.1532	0.1452	0.6488	0.0478	-0.0055	0.2579	-0.0505	0.4639	50.88	21.9195	-3.1649
15	2.1658	1.0206	-0.2184	6.8371	1.0551	2.8986	-0.1888	0.0694	-0.1948	0.1014	0.1018	-0.1049	0.5677	-0.146	0.078	0.4582	-0.024	0.0131	0.273	0.0046	0.2754	44.3248	-5.1108	-5.5852
16	6.1713	0.4256	-0.2581	2.5347	0.4852	4.9402	-0.2352	0.253	-0.141	-0.405	0.0647	0.0261	-0.4862	0.0717	0.1286	0.6406	0.0045	-0.0653	0.2624	0.0409	0.349	51.0099	15.9067	-14.3914
17	2.9051	-0.4221	1.3216	0.3685	-0.3609	2.9206	-0.2475	-0.1136	0.4402	0.1067	0.0273	-0.0792	-0.7688	-0.1222	0.2552	0.6535	0.0346	-0.0501	0.3289	-0.0575	0.4025	21.205	56.2676	30.853
18	5.8315	2.4198	-0.315	3.7371	-0.0874	2.065	-0.5319	0.5466	0.1359	-0.4633	0.4161	-0.174	-0.5304	0.2634	0.1636	0.5335	-0.1216	0.0066	0.4163	-0.0259	0.3399	29.7777	49.4123	28.9597
19	8.2694	5.9132	-0.3181	4.4455	-0.9328	2.3163	-0.1572	0.2063	-0.4555	-0.2506	0.1211	-0.4753	-0.2527	0.2771	0.277	0.3392	0.0289	0.0422	0.357	-0.0565	0.3833	28.4352	36.5056	33.8801
20	1.8457	-0.1297	1.7193	2.2749	-2.5716	6.8305	-0.1251	0.1233	0.0555	-0.3429	0.0631	-0.1379	-0.041	0.0733	0.0365	0.4937	0.0332	0.0408	0.2851	-0.0188	0.3214	21.8553	28.1292	22.3365
21	3.5101	-0.2125	-0.9278	3.0572	-0.1814	5.1692	0.0429	-0.037	0.1832	-0.1445	0.0419	-0.0649	-0.0585	0.2758	-0.0769	0.3024	0.0211	-0.0051	0.2735	-0.0062	0.322	25.0245	27.5703	32.6028
22	3.3937	0.0155	-1.9501	4.042	-1.005	7.2971	0.0239	0.0513	0.0659	-0.251	0.032	0.2289	0.0223	-0.4356	-0.0569	0.2685	0.0264	-0.0369	0.3004	-0.0032	0.2541	14.4612	29.1069	30.692
23	2.0257	1.4641	-0.717	2.8236	-0.2836	2.6897	0.0312	-0.227	-0.1124	0.1881	-0.069	-0.1948	-0.2307	0.1061	0.0045	0.3206	0.0419	-0.0041	0.311	-0.0067	0.3161	23.0577	39.1013	41.5075

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 89 through 129 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 130 through 154 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 155 through 197 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 198 through 227 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 228 through 274 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 275 through 293 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 294 through 340 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 96 through 154 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 155 through 184 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 185 through 197 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 198 through 227 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 228 through 250 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 251 through 274 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 275 through 293 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 294 through 322 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 323 through 339 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 96 through 154 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 155 through 184 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 185 through 197 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 198 through 222 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 223 through 250 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 251 through 293 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 294 through 338 )

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Protein , 1 types, 3 molecules ABC

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Non-polymers , 5 types, 490 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 3 molecules ABC

-
Non-polymers , 5 types, 490 molecules

-
Details

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
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

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Yorodumi