PDB-6auj: Crystal structure of thymidylate synthase from Elizabethkingia an...

ID or keywords:

Entry

Database: PDB / ID: 6auj

Title

Crystal structure of thymidylate synthase from Elizabethkingia anophelis NUHP1

Components

Thymidylate synthase

Keywords

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

Function / homology

Function and homology information

thymidylate synthase / thymidylate synthase activity / dTMP biosynthetic process / dTTP biosynthetic process / methylation / cytoplasm
Similarity search - Function

Biological species

Elizabethkingia anophelis NUHP1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.7 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of thymidylate synthase from Elizabethkingia anophelis NUHP1
Authors: Mayclin, S.J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Sep 1, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 27, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection / Derived calculations Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6auj.cif.gz	330 KB	Display	PDBx/mmCIF format
PDB format	pdb6auj.ent.gz	269.1 KB	Display	PDB format
PDBx/mmJSON format	6auj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6auj_validation.pdf.gz	469.5 KB	Display	wwPDB validaton report
Full document	6auj_full_validation.pdf.gz	476.3 KB	Display
Data in XML	6auj_validation.xml.gz	34.8 KB	Display
Data in CIF	6auj_validation.cif.gz	49.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/au/6auj ftp://data.pdbj.org/pub/pdb/validation_reports/au/6auj	HTTPS FTP

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Related structure data

Related structure data	3ix6S S: Starting model for refinement
Similar structure data	6pf4-1 4xsd-1 6pf6-1 6pf3-3 1f28-2 1dfm-d 3qs4-d 4xse-2 1kim-d 1hzw-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Thymidylate synthase

B: Thymidylate synthase

C: Thymidylate synthase

hetero molecules

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

1

A: Thymidylate synthase

hetero molecules

A: Thymidylate synthase

hetero molecules

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

2

B: Thymidylate synthase

C: Thymidylate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	144.110, 78.550, 73.370
Angle α, β, γ (deg.)	90.000, 90.490, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-465- HOH

#1: Protein	Thymidylate synthase / TSase Mass: 31252.545 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria) Gene: thyA, BD94_0762 / Plasmid: ElanA.00249.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A077EAN3, thymidylate synthase
#2: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 533 / 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: 2.22 Å³/Da / Density % sol: 44 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 23.2 mg/mL ElanA.00249.a.B1.PW38270 against MORPHEUS F9 (plate id 292618f9): 10% w/v PEG20000, 20% v/v PEG550 MME, 100 mM bicine/Trizma base, pH 8.5, 20 mM D-glucose, 20 mM D-mannose, 20 mM ...Details: 23.2 mg/mL ElanA.00249.a.B1.PW38270 against MORPHEUS F9 (plate id 292618f9): 10% w/v PEG20000, 20% v/v PEG550 MME, 100 mM bicine/Trizma base, pH 8.5, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetryl-D-glucosamine, cryoprotection: direct, puck id zfj8-8

Crystal

Density Matthews: 2.22 Å³/Da / Density % sol: 44 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 23.2 mg/mL ElanA.00249.a.B1.PW38270 against MORPHEUS F9 (plate id 292618f9): 10% w/v PEG20000, 20% v/v PEG550 MME, 100 mM bicine/Trizma base, pH 8.5, 20 mM D-glucose, 20 mM D-mannose, 20 mM ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2017

Radiation

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

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.7→50 Å / Num. obs: 89735 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.301 % / B_iso Wilson estimate: 28.64 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.056 / R_rim(I) all: 0.064 / Χ²: 1.043 / Net I/σ(I): 13.36

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
1.7-1.74	3.848	0.576	2.01	6648	0.819	0.669	100
1.74-1.79	4.335	0.417	3.03	6446	0.922	0.475	100
1.79-1.84	4.412	0.323	4.01	6275	0.946	0.368	100
1.84-1.9	4.411	0.254	5.16	6087	0.961	0.289	100
1.9-1.96	4.421	0.181	7.04	5920	0.981	0.207	99.9
1.96-2.03	4.405	0.135	9.3	5729	0.987	0.153	99.9
2.03-2.11	4.401	0.111	11.06	5540	0.99	0.126	99.9
2.11-2.19	4.383	0.092	13.4	5293	0.992	0.105	99.9
2.19-2.29	4.378	0.081	15.04	5112	0.994	0.092	99.9
2.29-2.4	4.359	0.075	16.76	4870	0.993	0.085	99.8
2.4-2.53	4.332	0.064	18.96	4609	0.995	0.073	99.8
2.53-2.69	4.304	0.06	20.2	4396	0.995	0.069	99.7
2.69-2.87	4.277	0.057	21.76	4111	0.995	0.065	99.7
2.87-3.1	4.241	0.054	22.89	3831	0.995	0.062	99.3
3.1-3.4	4.22	0.051	24.02	3525	0.995	0.059	99.1
3.4-3.8	4.211	0.049	24.93	3220	0.996	0.056	99.5
3.8-4.39	4.25	0.047	25.25	2816	0.996	0.053	99.3
4.39-5.38	4.262	0.045	25.69	2398	0.997	0.051	99.4
5.38-7.6	4.286	0.042	25.65	1874	0.996	0.049	99.6
7.6-50	3.787	0.045	24.28	1035	0.993	0.053	96.7

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3IX6

3ix6

Resolution: 1.7→50 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.8

	R_factor	Num. reflection	% reflection
R_free	0.1758	2208	2.46 %
R_work	0.1571	-	-
obs	0.1576	89704	99.73 %

Solvent computation

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

Displacement parameters

B_iso max: 119.64 Å² / B_iso mean: 39.899 Å² / B_iso min: 17.65 Å²

Refinement step

Cycle: final / Resolution: 1.7→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5964	0	30	537	6531
B_iso mean	-	-	63.7	44.73	-
Num. residues	-	-	-	-	757

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6268
X-RAY DIFFRACTION	f_angle_d	0.857	8556
X-RAY DIFFRACTION	f_chiral_restr	0.054	940
X-RAY DIFFRACTION	f_plane_restr	0.005	1105
X-RAY DIFFRACTION	f_dihedral_angle_d	13.409	3695

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 16

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.7-1.7369	0.2943	127	0.2737	5476	5603	100
1.7369-1.7773	0.267	144	0.2272	5436	5580	100
1.7773-1.8218	0.2017	132	0.2044	5489	5621	100
1.8218-1.871	0.2084	138	0.1855	5431	5569	100
1.871-1.9261	0.2216	136	0.1717	5436	5572	100
1.9261-1.9883	0.1936	164	0.1708	5436	5600	100
1.9883-2.0593	0.2065	92	0.1725	5521	5613	100
2.0593-2.1418	0.1944	150	0.173	5430	5580	100
2.1418-2.2392	0.1913	137	0.167	5490	5627	100
2.2392-2.3572	0.172	152	0.1621	5435	5587	100
2.3572-2.5049	0.2179	126	0.165	5468	5594	100
2.5049-2.6982	0.1877	117	0.1661	5498	5615	100
2.6982-2.9696	0.1942	127	0.1717	5471	5598	99
2.9696-3.399	0.176	137	0.1651	5469	5606	99
3.399-4.2811	0.1714	154	0.1314	5481	5635	99
4.2811-34.633	0.1357	175	0.1345	5529	5704	99

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	2.0344	0.5424	-0.6328	1.7158	-0.761	3.5599	0.148	-0.285	0.008	0.2167	-0.0361	-0.1276	0.1943	0.3508	-0.0835	0.2313	0.0146	-0.0541	0.2983	-0.0405	0.2383	29.0697	-69.4458	32.8714
2	3.2433	1.3201	-1.6154	1.9181	-2.7456	6.7683	0.2377	-0.1251	0.0451	0.2454	-0.2506	-0.5004	-0.2897	1.4195	0.1235	0.269	-0.0391	-0.0204	0.4631	-0.118	0.4247	42.3895	-60.9809	27.8111
3	4.1675	-0.3136	1.9956	4.0152	-0.1997	7.1091	0.0708	-0.9193	-0.0043	0.7725	-0.0552	-0.1946	-0.0868	-0.0121	-0.1282	0.5145	-0.0793	-0.0546	0.4805	-0.0241	0.2375	26.7069	-65.9946	49.2659
4	2.4483	-0.5564	1.9218	5.3687	2.3883	6.4339	0.2253	0.189	0.4818	-0.0782	-0.2645	0.1862	-0.3087	-0.3051	0.0551	0.4297	0.1412	0.2648	0.3305	0.0606	0.6943	-15.7568	-28.3312	-0.0711
5	0.5726	-0.2991	-0.4874	1.8371	-0.2967	1.9427	0.1639	-0.1618	0.3178	0.3289	0.1205	0.1403	-0.4557	-0.2329	-0.2203	0.2903	0.0087	0.1819	0.2882	-0.0282	0.3976	-8.2665	-37.0044	12.858
6	3.3773	-0.5584	-1.3458	1.6173	0.739	3.3493	-0.0091	0.0244	-0.1198	0.3972	0.0198	0.4834	0.3142	-0.5688	-0.0291	0.2138	-0.0512	0.068	0.2446	0.0445	0.2894	-10.4081	-55.8477	12.1268
7	1.0886	-0.2803	-0.3818	1.7513	-0.263	1.9864	0.172	-0.1802	0.2724	0.2428	0.0147	0.0311	-0.2793	0.0742	-0.1562	0.2025	-0.0389	0.0966	0.183	-0.0383	0.254	0.2348	-42.5567	9.6997
8	3.4122	-4.3563	-3.5079	6.3295	3.5704	4.6527	0.3046	0.1578	0.4175	-0.1224	-0.1534	0.34	-0.2028	-0.7902	0.1585	0.3586	0.1541	0.2418	0.4429	0.0948	0.6194	-20.8897	-28.0639	3.7741
9	2.9345	-2.646	0.3369	6.3391	-0.161	2.3643	-0.1081	-0.6532	0.4963	1.0471	0.2771	0.0461	-0.3864	-0.0608	-0.182	0.4969	-0.0414	0.155	0.4116	-0.1212	0.3421	-4.1435	-37.9778	25.9014
10	2.1636	-1.101	2.5871	3.0222	-0.1088	3.8202	0.2861	-0.0805	-0.5683	-0.3083	-0.3505	0.0007	0.9713	0.3164	0.0087	0.5438	0.1243	-0.142	0.3334	0.0095	0.4321	28.7955	-91.1193	23.2089
11	0.893	-0.3322	0.1881	2.8272	-1.1905	4.1083	0.2494	0.2752	-0.3437	-0.7325	-0.0764	-0.0039	0.9934	0.2683	-0.0894	0.4852	0.1545	-0.078	0.3565	-0.0611	0.3528	28.0689	-84.9353	12.4337
12	2.841	0.4515	0.0423	4.3291	1.4025	2.383	0.4191	-0.0096	-0.5937	-0.0114	-0.1601	0.3084	0.919	-0.431	-0.1668	0.4913	-0.0895	-0.2151	0.278	0.018	0.3754	5.5917	-82.7765	9.4655
13	1.7381	-1.1764	-0.2313	9.4406	4.4983	7.5222	0.1793	-0.1027	-0.1641	0.1996	-0.1819	0.4338	0.1239	-0.5896	0.0494	0.1297	-0.019	-0.0316	0.2173	0.0231	0.204	5.8511	-66.3562	15.918
14	2.3635	0.1023	-0.0022	2.2686	-1.0809	3.7814	0.126	0.0226	0.0324	-0.1578	-0.0738	0.0209	0.1424	0.0789	-0.0542	0.1801	0.0101	-0.0246	0.1799	-0.0243	0.17	17.1628	-67.0342	14.5964
15	1.3297	-0.1753	-0.2247	1.808	-0.223	2.0002	0.2802	0.2638	-0.3323	-0.3857	-0.169	-0.027	0.8053	0.394	0.0026	0.4805	0.1393	-0.0859	0.2657	-0.0658	0.2771	23.1594	-82.3214	7.6695
16	4.7553	1.74	-1.6548	2.5956	0.7248	6.4433	0.0122	0.0635	0.2215	-0.2009	-0.0293	-0.2911	-0.1442	0.6433	-0.1627	0.229	-0.0144	0.0685	0.5145	-0.0609	0.4382	40.3395	-61.7079	17.5466
17	2.3581	2.0472	-1.7025	2.3333	-0.3547	4.8623	0.1336	-0.0784	-0.0838	0.25	0.0282	-0.3681	0.2631	0.7496	0.0495	0.1933	0.0866	-0.0377	0.3332	-0.05	0.2852	35.9491	-70.1009	24.5291
18	2.0304	-0.2176	0.6033	2.0414	-0.0636	3.1643	0.0711	-0.2671	0.1571	0.1925	-0.0254	-0.0322	-0.0717	-0.0152	-0.0344	0.1782	-0.0345	0.0323	0.2396	-0.0319	0.1666	19.1357	-63.0578	33.6511

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 166 through 212 )	C	166 - 212
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 213 through 240 )	C	213 - 240
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 241 through 259 )	C	241 - 259
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 8 through 32 )	A	8 - 32
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 33 through 72 )	A	33 - 72
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 73 through 118 )	A	73 - 118
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 119 through 212 )	A	119 - 212
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 213 through 229 )	A	213 - 229
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 230 through 259 )	A	230 - 259
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 8 through 32 )	B	8 - 32
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 33 through 60 )	B	33 - 60
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 61 through 101 )	B	61 - 101
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 102 through 118 )	B	102 - 118
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 119 through 165 )	B	119 - 165
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 166 through 265 )	B	166 - 265
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 9 through 32 )	C	9 - 32
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 33 through 48 )	C	33 - 48
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 49 through 165 )	C	49 - 165

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