PDB-6oew: Structure of a Cytidylyltransferase from Leptospira borgpeterseni...

ID or keywords:

Entry

Database: PDB / ID: 6oew

Title

Structure of a Cytidylyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)

Components

Cytidylyltransferase

Keywords

TRANSFERASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Acylneuraminate cytidylyltransferase / Cytidylyltransferase / nucleotidyltransferase activity / Nucleotide-diphospho-sugar transferases / Cytidylyltransferase

Function and homology information

Biological species

Leptospira borgpetersenii serovar Hardjo-bovis

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Structure of a Cytidylyltransferase from Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197)
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Mar 27, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 17, 2019	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6oew.cif.gz	221.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6oew.ent.gz	177.6 KB	Display	PDB format
PDBx/mmJSON format	6oew.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6oew_validation.pdf.gz	449.6 KB	Display	wwPDB validaton report
Full document	6oew_full_validation.pdf.gz	450.6 KB	Display
Data in XML	6oew_validation.xml.gz	22.8 KB	Display
Data in CIF	6oew_validation.cif.gz	33.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oe/6oew ftp://data.pdbj.org/pub/pdb/validation_reports/oe/6oew	HTTPS FTP

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Related structure data

Similar structure data	2mqn-d 3bhm-d 5hw1-4 5qa4-3 5qab-2 4rva-d 1axb-d 4bku-d 4jp2-d 2afy-d 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
Other databases	TargetTrack: SSGCID-LpboA.19557.c

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (1) #254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Cytidylyltransferase

B: Cytidylyltransferase

hetero molecules

59 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Cytidylyltransferase

hetero molecules

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

2

B: Cytidylyltransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	65.510, 65.510, 261.930
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-544- HOH

#1: Protein	Cytidylyltransferase Mass: 29265.590 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197) (bacteria) Strain: JB197 / Gene: LBJ_1129 / Plasmid: LpboA.19557.c.B1 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) Strain (production host): BL21(DE3) / References: UniProt: Q04TM9
#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 361 / 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: 2.4 Å³/Da / Density % sol: 48.9 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Molecular Dimensions Morpheus screen, a6: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30mM of each magnesium chloride and calcium chloride, 100mM MOPS/HEPES-Na pH 7.5: LpboA.19557.c.B1. ...Details: Molecular Dimensions Morpheus screen, a6: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30mM of each magnesium chloride and calcium chloride, 100mM MOPS/HEPES-Na pH 7.5: LpboA.19557.c.B1.PS38542 at 24.74mg/ml: cryo: direct: tray 306886 a6: puck ogn0-8. For experimental phasing, a crystal from Morpheus screen a3 (10% w/v PEG 4000, 20% v/v glycerol, 30mM of each magnesium chloride and calcium chloride, 100mM MES/imidazole pH 6.5: LpboA.19557.c.B1.PS38542 at 24.74mg/ml) was incubated for 20sec in a solution of 92.5% reservoir and 7.5% 5M Sodium iodide in ethylene glycol, and vitrified: tray: 306886 a3: puck: kzx0-4

Crystal

Density Matthews: 2.4 Å³/Da / Density % sol: 48.9 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions Morpheus screen, a6: 10% w/v PEG 8000, 20% v/v ethylene glycol, 30mM of each magnesium chloride and calcium chloride, 100mM MOPS/HEPES-Na pH 7.5: LpboA.19557.c.B1. ...

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID	Serial crystal experiment
1	100	1	N
2	100	1	N

Diffraction source

Source	Site	Beamline	Type	ID	Wavelength (Å)
SYNCHROTRON	APS	21-ID-F		1	0.97872
ROTATING ANODE			RIGAKU FR-E+ SUPERBRIGHT	2	1.5418

Detector

Type	ID	Detector	Date
RAYONIX MX-300	1	CCD	Feb 28, 2019
RIGAKU SATURN 944+	2	CCD	Mar 1, 2019

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	C(111)	SINGLE WAVELENGTH	M	x-ray	1
2	RIGAKU VARIMAX	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97872	1
2	1.5418	1

Reflection

Resolution: 1.85→43.671 Å / Num. obs: 50144 / % possible obs: 100 % / Redundancy: 9.57 % / B_iso Wilson estimate: 38.04 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.054 / R_rim(I) all: 0.057 / Χ²: 1.045 / Net I/σ(I): 22.16

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	9.747	0.581	3.27	3620	0.954	0.614	100
1.9-1.95	9.714	0.434	4.44	3547	0.97	0.458	99.9
1.95-2.01	9.73	0.342	5.69	3451	0.98	0.361	100
2.01-2.07	9.74	0.253	7.67	3332	0.988	0.266	100
2.07-2.14	9.737	0.206	9.31	3252	0.992	0.218	100
2.14-2.21	9.696	0.152	12.32	3155	0.995	0.16	100
2.21-2.29	9.711	0.143	13.75	3040	0.995	0.151	100
2.29-2.39	9.696	0.116	16.97	2942	0.997	0.122	100
2.39-2.49	9.65	0.097	19.65	2815	0.997	0.102	100
2.49-2.62	9.634	0.081	23.55	2727	0.998	0.085	100
2.62-2.76	9.622	0.068	27.15	2589	0.999	0.072	100
2.76-2.93	9.603	0.059	31.27	2441	0.999	0.063	100
2.93-3.13	9.521	0.05	36.68	2336	0.999	0.052	100
3.13-3.38	9.534	0.044	42.34	2160	0.999	0.046	100
3.38-3.7	9.402	0.039	46.75	2011	0.999	0.042	100
3.7-4.14	9.363	0.036	49.96	1830	0.999	0.039	100
4.14-4.78	9.239	0.035	52.08	1643	0.999	0.037	100
4.78-5.85	9.06	0.034	51.43	1419	0.999	0.036	100
5.85-8.27	8.702	0.033	50.02	1136	0.999	0.035	100
8.27-43.671	7.493	0.033	48.1	698	0.999	0.035	97.6

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	(1.15rc1_3423)	refinement
PDB_EXTRACT	3.24	data extraction
PHASER		phasing
PARROT		phasing
ARP/wARP		model building
BUCCANEER		model building
Coot		model building

Refinement

Method to determine structure:

SAD / Resolution: 1.85→43.671 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.59

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2147	1946	3.89 %	0
R_work	0.1714	-	-	-
obs	0.1731	49962	99.86 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 106.64 Å² / B_iso mean: 41.3441 Å² / B_iso min: 22.24 Å²

Refinement step

Cycle: final / Resolution: 1.85→43.671 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3860	0	28	366	4254
B_iso mean	-	-	48.96	47.61	-
Num. residues	-	-	-	-	477

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	4002
X-RAY DIFFRACTION	f_angle_d	0.989	5412
X-RAY DIFFRACTION	f_dihedral_angle_d	15.228	2450
X-RAY DIFFRACTION	f_chiral_restr	0.06	623
X-RAY DIFFRACTION	f_plane_restr	0.005	694

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
1.85-1.8963	0.3195	130	0.2492	3344	3474
1.8963-1.9475	0.2803	137	0.2198	3341	3478
1.9475-2.0049	0.2778	128	0.2024	3375	3503
2.0049-2.0696	0.253	133	0.1876	3370	3503
2.0696-2.1435	0.2298	146	0.193	3371	3517
2.1435-2.2293	0.2298	140	0.1733	3369	3509
2.2293-2.3308	0.2413	133	0.179	3410	3543
2.3308-2.4537	0.2332	136	0.182	3392	3528
2.4537-2.6074	0.2264	139	0.1846	3407	3546
2.6074-2.8087	0.2778	123	0.1873	3464	3587
2.8087-3.0913	0.2191	147	0.1829	3445	3592
3.0913-3.5384	0.2162	158	0.1772	3428	3586
3.5384-4.4573	0.1785	156	0.1415	3538	3694
4.4573-43.6834	0.1868	140	0.1588	3762	3902

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	0.8775	-0.4712	0.8594	3.1985	-0.1769	0.9231	-0.1474	-0.0182	0.5156	0.119	-0.1499	0.5085	-1.3074	-0.8094	0.146	0.6494	0.2436	-0.1105	0.3946	-0.0539	0.4264	6.9865	30.3664	72.8873
2	5.0202	-0.7462	0.232	6.7684	0.3385	4.3003	-0.1154	0.1747	0.1344	0.0971	-0.07	0.5576	-0.5171	-0.7729	0.1412	0.2457	0.1046	-0.056	0.3865	-0.0791	0.2856	3.9996	17.9367	66.9506
3	4.801	0.8125	1.96	0.3815	0.0534	3.5183	0.1039	-0.0428	-0.246	0.2722	-0.0135	-0.142	0.1034	0.0472	-0.0584	0.3128	0.0262	-0.0714	0.1803	-0.0249	0.3028	21.7822	7.6903	81.5061
4	3.8051	1.7056	-1.2018	2.8993	0.223	3.6698	0.1266	0.7157	-0.6297	-0.4887	0.0138	-0.1816	0.2267	0.2158	-0.0155	0.378	0.1227	-0.0457	0.3249	-0.0679	0.3894	26.5201	3.653	71.0138
5	7.7575	0.1283	-3.7657	3.1844	1.2135	6.4576	0.2622	-0.0388	-0.1359	0.1488	-0.3012	-0.0806	0.1475	-0.0209	-0.0045	0.3693	-0.0017	-0.1068	0.2159	0.0026	0.3569	17.0598	3.9406	87.0017
6	1.034	0.1433	-0.1952	3.5484	-2.9488	5.0432	0.2636	0.1107	-0.2135	0.0301	0.2703	0.147	0.0141	-0.1711	-0.3531	0.4028	0.0269	-0.1085	0.1863	-0.0063	0.2906	1.325	-3.3268	90.998
7	1.4627	-0.3512	-0.3149	1.759	0.2045	5.1057	0.1854	0.0255	-0.1858	0.2446	-0.0051	-0.5994	0.5412	0.3864	-0.2625	0.3921	0.0669	-0.1378	0.1893	-0.0569	0.4148	8.2648	-14.3684	90.6052
8	3.2904	0.6197	1.3389	3.9592	2.5755	8.5995	0.0032	0.016	0.0761	0.2454	-0.0681	-0.4731	-0.3584	0.3775	0.0845	0.3319	0.0332	-0.0426	0.1667	0.0273	0.2947	9.5367	-2.4628	90.8606
9	2.3522	0.6472	1.9597	0.4301	0.8835	3.5193	-0.0596	0.0436	0.1831	-0.0341	-0.069	-0.0189	-0.3485	-0.0594	0.1215	0.4334	0.0538	-0.0566	0.1934	-0.0142	0.2689	-0.2863	-1.6119	84.2388
10	4.5032	0.6781	2.0619	4.773	-0.0272	4.8097	-0.0355	-0.2283	-0.0473	0.3927	0.0774	-0.0864	0.0868	-0.4574	-0.0219	0.3989	0.0495	-0.0573	0.2846	-0.0738	0.253	-11.6112	-7.9822	82.7268
11	1.6041	0.1662	0.1624	2.0243	-0.187	1.9475	-0.048	-0.331	0.4553	0.0908	0.066	0.2391	-0.7052	-0.435	-0.0607	0.6021	0.175	-0.0752	0.2872	-0.0685	0.3727	-9.8329	5.9375	89.8158
12	3.9523	-0.0499	0.9735	6.0794	0.9433	4.2191	0.1518	0.0288	0.2142	-0.0394	-0.4491	0.7653	-0.5198	-0.9112	0.2829	0.4631	0.1848	-0.0127	0.4018	-0.0802	0.3538	-17.6701	0.4665	85.2811
13	3.8262	-0.9323	3.2775	3.3725	-2.4995	5.9781	0.5958	0.0071	-0.4599	0.112	-0.0475	0.2795	1.2161	-0.6003	-0.5138	0.6065	-0.0427	-0.1445	0.3547	-0.0214	0.4195	-9.5223	-19.0641	88.7679
14	1.4051	-0.4492	0.242	4.5905	0.7652	3.4334	0.1767	-0.1433	-0.5665	-0.0039	-0.2117	0.1029	1.1655	-0.2311	0.0496	0.8058	0.0062	-0.2003	0.2702	-0.0289	0.499	-1.2544	-26.0699	91.845
15	3.5291	0.1538	-0.3587	3.3864	-1.0982	7.47	-0.033	0.3569	0.1674	-0.1582	0.1431	0.1151	-1.1061	-0.2018	-0.0944	0.3759	-0.0016	-0.0316	0.1499	-0.0025	0.2576	20.4621	25.4661	76.347
16	2.5382	-0.1631	0.3706	2.0903	0.29	4.0999	0.0111	0.2915	-0.0744	-0.0481	-0.0053	-0.1996	-0.2743	0.5551	-0.0773	0.2895	-0.0272	-0.0546	0.3153	-0.0118	0.3026	30.2107	17.4246	76.4591
17	3.5346	0.1253	0.2113	3.1027	1.8967	5.8113	-0.1518	0.2166	0.2353	-0.1869	-0.0289	-0.2376	-0.9828	0.3932	0.1547	0.4273	-0.0732	-0.0372	0.2485	0.0741	0.2683	27.823	28.8919	75.022
18	2.0295	0.1625	1.2605	1.504	0.5586	3.244	-0.1758	0.3122	0.2608	-0.2109	0.0137	0.0223	-0.7594	0.21	0.1627	0.4271	-0.0117	-0.0374	0.2373	0.0265	0.2396	18.7316	26.1363	68.4319
19	3.2685	0.2709	2.1417	2.3793	-0.4013	4.8048	-0.1214	0.0948	0.1389	-0.1227	0.1553	0.0811	-0.4475	-0.3911	-0.0046	0.3364	0.0757	-0.0368	0.2897	-0.0604	0.2572	10.0303	16.5376	66.5957

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 141 through 165 )	B	141 - 165
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 166 through 184 )	B	166 - 184
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 185 through 208 )	B	185 - 208
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 209 through 225 )	B	209 - 225
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 226 through 238 )	B	226 - 238
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 0 through 18 )	A	0 - 18
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 19 through 39 )	A	19 - 39
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 40 through 65 )	A	40 - 65
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 66 through 119 )	A	66 - 119
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 120 through 140 )	A	120 - 140
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 141 through 163 )	A	141 - 163
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 164 through 179 )	A	164 - 179
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 180 through 195 )	A	180 - 195
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 196 through 237 )	A	196 - 237
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 0 through 18 )	B	0 - 18
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 19 through 39 )	B	19 - 39
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 40 through 65 )	B	40 - 65
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 66 through 119 )	B	66 - 119
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 120 through 140 )	B	120 - 140

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About Yorodumi

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Yorodumi