PDB-5usw: The crystal structure of 7,8-dihydropteroate synthase from Vibrio...

ID or keywords:

Entry

Database: PDB / ID: 5usw

Title

The crystal structure of 7,8-dihydropteroate synthase from Vibrio fischeri ES114

Components

Dihydropteroate synthase

Keywords

TRANSFERASE / 7 / 8-dihydropteroate synthase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

dihydropteroate synthase / dihydropteroate synthase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Vibrio fischeri (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.643 Å

Authors

Tan, K. / Zhou, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The crystal structure of 7,8-dihydropteroate synthase from Vibrio fischeri ES114
Authors: Tan, K. / Zhou, M. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Feb 14, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 22, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 23, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2	Sep 13, 2017	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Nov 27, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4	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 1.5	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5usw.cif.gz	448.2 KB	Display	PDBx/mmCIF format
PDB format	pdb5usw.ent.gz	369.6 KB	Display	PDB format
PDBx/mmJSON format	5usw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5usw_validation.pdf.gz	490.8 KB	Display	wwPDB validaton report
Full document	5usw_full_validation.pdf.gz	501.9 KB	Display
Data in XML	5usw_validation.xml.gz	48.6 KB	Display
Data in CIF	5usw_validation.cif.gz	71.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/us/5usw ftp://data.pdbj.org/pub/pdb/validation_reports/us/5usw	HTTPS FTP

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Related structure data

Related structure data	5jq9S S: Starting model for refinement
Similar structure data	1zcv-1 6p53-d 6hzj-d 1zcy-1 3q4s-1 5vrb-3 6dk8-2 3u2t-1 1ll3-1 6nna-1 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: IDP07359

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Dihydropteroate synthase

B: Dihydropteroate synthase

C: Dihydropteroate synthase

D: Dihydropteroate synthase

hetero molecules

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

1

A: Dihydropteroate synthase

B: Dihydropteroate synthase

hetero molecules

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

2

C: Dihydropteroate synthase

D: Dihydropteroate synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	91.953, 65.881, 94.942
Angle α, β, γ (deg.)	90.00, 105.83, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase Mass: 31330.225 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio fischeri (strain ATCC 700601 / ES114) (bacteria) Strain: ATCC 700601 / ES114 / Gene: folP, VF_0480 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5E7M1, dihydropteroate synthase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH₂O₂
#4: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 822 / 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: 2.25 Å³/Da / Density % sol: 45.29 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M potassium sodium tartrate, 20% w/v PEG3350

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
Detector	Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Feb 8, 2017 / Details: mirror
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97918 Å / Relative weight: 1
Reflection	Resolution: 1.64→50 Å / Num. obs: 130804 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / B_iso Wilson estimate: 11.5 Å² / R_merge(I) obs: 0.055 / R_pim(I) all: 0.037 / Χ²: 0.586 / Net I/σ(I): 13.8
Reflection shell	Resolution: 1.64→1.67 Å / Redundancy: 2.8 % / R_merge(I) obs: 0.831 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6479 / Num. unique obs: 6479 / R_pim(I) all: 0.592 / Χ²: 0.812 / % possible all: 97.7

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Processing

Software

Name	Version	Classification
PHENIX	(1.11.1_2575: ???)	refinement
HKL-3000		data reduction
HKL-3000		data scaling
HKL-3000		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 5JQ9

5jq9

Resolution: 1.643→36.13 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.48

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.204	6159	5 %	random
R_work	0.1713	-	-	-
obs	0.1729	123109	92.47 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.643→36.13 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8301	0	70	822	9193

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.014	8738
X-RAY DIFFRACTION	f_angle_d	1.268	11823
X-RAY DIFFRACTION	f_dihedral_angle_d	6.75	7345
X-RAY DIFFRACTION	f_chiral_restr	0.077	1382
X-RAY DIFFRACTION	f_plane_restr	0.008	1535

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 (%)
1.6426-1.6613	0.2535	125	0.2146	2700	X-RAY DIFFRACTION	65
1.6613-1.6808	0.2583	144	0.2137	3042	X-RAY DIFFRACTION	72
1.6808-1.7013	0.2091	168	0.2055	3089	X-RAY DIFFRACTION	74
1.7013-1.7229	0.2348	173	0.1997	3298	X-RAY DIFFRACTION	79
1.7229-1.7455	0.2358	164	0.2172	3501	X-RAY DIFFRACTION	83
1.7455-1.7694	0.2541	180	0.206	3511	X-RAY DIFFRACTION	84
1.7694-1.7947	0.2695	182	0.2049	3605	X-RAY DIFFRACTION	86
1.7947-1.8215	0.2592	197	0.1949	3732	X-RAY DIFFRACTION	89
1.8215-1.85	0.2322	216	0.1876	3785	X-RAY DIFFRACTION	91
1.85-1.8803	0.2059	202	0.188	3913	X-RAY DIFFRACTION	93
1.8803-1.9127	0.2135	202	0.1891	3986	X-RAY DIFFRACTION	95
1.9127-1.9475	0.1977	206	0.1879	4073	X-RAY DIFFRACTION	97
1.9475-1.9849	0.2316	188	0.1807	4164	X-RAY DIFFRACTION	98
1.9849-2.0255	0.2083	195	0.1833	4135	X-RAY DIFFRACTION	99
2.0255-2.0695	0.2045	210	0.1866	4120	X-RAY DIFFRACTION	98
2.0695-2.1176	0.212	219	0.1781	4111	X-RAY DIFFRACTION	98
2.1176-2.1706	0.2081	217	0.1712	4066	X-RAY DIFFRACTION	97
2.1706-2.2293	0.2129	240	0.1674	4149	X-RAY DIFFRACTION	99
2.2293-2.2948	0.215	193	0.1659	4212	X-RAY DIFFRACTION	99
2.2948-2.3689	0.2166	227	0.1635	4197	X-RAY DIFFRACTION	99
2.3689-2.4535	0.1821	233	0.1639	4165	X-RAY DIFFRACTION	99
2.4535-2.5518	0.2073	242	0.1668	4173	X-RAY DIFFRACTION	100
2.5518-2.6679	0.216	244	0.1708	4153	X-RAY DIFFRACTION	100
2.6679-2.8085	0.2299	238	0.1745	4182	X-RAY DIFFRACTION	99
2.8085-2.9843	0.2119	232	0.17	4143	X-RAY DIFFRACTION	98
2.9843-3.2146	0.1961	215	0.1688	4090	X-RAY DIFFRACTION	97
3.2146-3.5379	0.1714	243	0.1475	4193	X-RAY DIFFRACTION	99
3.5379-4.0492	0.1779	225	0.1457	4174	X-RAY DIFFRACTION	99
4.0492-5.0993	0.1517	222	0.1424	4186	X-RAY DIFFRACTION	98
5.0993-36.1385	0.2251	217	0.1882	4102	X-RAY DIFFRACTION	94

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	0.4024	-0.3187	0.1565	0.9035	0.1224	0.2705	-0.0419	-0.031	0.0593	0.0497	0.0348	-0.0418	-0.022	0.0133	0.0012	0.1069	0.0077	0.0143	0.1543	0.0058	0.0677	52.0951	51.1485	55.0885
2	2.3208	-0.6803	-0.8359	2.3233	-1.4741	1.6954	-0.0116	-0.0451	0.0597	-0.0541	0.0128	-0.4738	0.0997	0.391	-0.0939	0.1249	0.016	0.0028	0.2397	-0.0134	0.1667	71.4546	20.8106	49.2356
3	2.517	-1.987	0.2817	1.9296	0.8264	3.0523	0.1342	0.1704	-0.2551	-0.3092	-0.2539	0.1088	0.196	-0.3301	-0.0116	0.1811	-0.0176	0.0406	0.25	-0.0175	0.1864	67.7946	18.4715	39.1828
4	4.4312	0.3883	-2.4348	6.1899	-1.604	3.5471	-0.2406	0.2505	-0.225	-0.6812	0.1411	-0.0036	0.393	0.0162	0.0835	0.1741	0.0093	0.0289	0.2145	-0.0093	0.1217	73.2126	9.8078	42.1356
5	1.617	-0.235	-0.5853	0.5476	0.5849	0.6863	-0.14	-0.1301	-0.1978	0.069	0.0752	0.0323	0.1188	0.1044	0.0587	0.1352	0.0258	0.0206	0.1673	0.0347	0.098	56.9358	17.0165	55.4551
6	4.667	1.3141	3.2215	7.2069	5.4767	7.6652	0.0477	-0.0177	0.045	0.0963	-0.0013	-0.3331	0.0296	0.0465	-0.0237	0.0589	0.0014	-0.0063	0.1033	0.0458	0.1413	64.9896	35.9623	51.7212
7	1.2836	-0.4279	0.0416	1.0097	0.4356	0.4477	0.0088	0.0379	-0.0832	-0.0174	0.008	0.1206	-0.0011	-0.0642	-0.0541	0.0894	-0.0172	0.0008	0.0686	0.0127	0.0939	29.1321	20.207	88.0095
8	0.4894	-0.8213	-0.0986	1.812	-0.5101	1.7754	0.1205	0.0826	0.1043	-0.0958	-0.0585	-0.1874	-0.2102	0.3192	-0.0598	0.1079	-0.0345	0.0282	0.1186	0.0169	0.096	33.6931	21.671	79.4141
9	1.2454	-0.107	0.7325	1.9752	0.6158	2.4938	-0.0206	0.0956	0.1521	-0.0983	-0.037	-0.0159	-0.1662	0.0123	0.0441	0.0721	0.0125	0.0167	0.045	0.0057	0.094	28.7974	30.3092	89.3549
10	5.4653	-3.7845	2.2255	3.4239	-1.3506	1.3894	-0.3848	-0.1042	0.2216	0.425	0.1648	-0.0961	-0.2389	0.0485	0.1982	0.1607	-0.012	-0.009	0.1108	-0.0263	0.1118	43.1114	26.5033	110.8835
11	0.8733	-0.2959	0.3476	1.3887	0.2893	0.2951	-0.0189	0.0206	0.0581	0.0554	0.0258	-0.0051	-0.0485	0.0254	-0.0153	0.0869	-0.0083	0.0233	0.0441	0.0159	0.0603	40.1012	13.1572	98.3058
12	3.1414	-1.0564	-1.1867	2.5841	-1.0234	2.4361	-0.0327	-0.1611	-0.203	-0.0217	-0.0727	-0.1315	-0.0816	0.2541	0.009	0.0674	-0.0201	0.004	0.0957	0.0274	0.121	57.921	-11.0917	95.2324
13	1.0921	-0.19	0.882	1.5167	1.0511	1.7985	0.0712	0.2366	-0.2415	-0.1072	-0.1822	0.0988	0.1808	-0.1289	0.051	0.1217	-0.0025	0.0379	0.1606	-0.0542	0.1308	54.0896	-13.771	84.7576
14	1.4397	0.1982	-0.8501	1.8	-0.8304	2.0057	-0.1483	0.0339	-0.4554	-0.14	0.0058	-0.0794	0.2645	0.0988	0.0629	0.1039	0.0191	0.036	0.071	0.0142	0.1928	57.8348	-23.2219	92.2487
15	4.0368	-2.9747	-0.0934	3.0403	0.0252	0.7713	-0.2251	-0.0654	-0.3512	0.2702	0.0198	0.082	0.1151	0.0393	0.1723	0.1255	-0.013	0.0321	0.0961	0.0613	0.1563	39.0355	-20.3387	109.327
16	1.5031	-0.1436	-0.1361	1.2108	-0.1831	0.2729	0.0081	-0.0033	-0.0625	0.0306	-0.008	-0.015	0.0381	0.0141	-0.0103	0.0745	-0.0051	0.0115	0.0402	0.0151	0.0592	44.3628	-6.4214	97.9626
17	1.4137	0.2864	-1.0672	1.8653	-1.3507	4.2427	0.0697	-0.0374	0.0142	-0.0472	-0.0799	0.0191	-0.0856	0.0917	0.0197	0.0768	-0.0036	-0.0036	0.12	0.0048	0.0789	42.8259	51.8615	39.292
18	2.2362	0.4569	1.4762	4.3397	0.8198	3.5894	-0.036	0.0421	0.1461	-0.2305	-0.0775	-0.0149	-0.293	-0.0935	0.0965	0.1114	0.048	0.008	0.1215	0.0073	0.055	39.9553	60.9907	39.3395

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 110 through 278 )
2	X-RAY DIFFRACTION	2	chain 'D' and (resid 0 through 36 )
3	X-RAY DIFFRACTION	3	chain 'D' and (resid 37 through 70 )
4	X-RAY DIFFRACTION	4	chain 'D' and (resid 71 through 109 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 110 through 258 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 259 through 277 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 0 through 33 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 34 through 70 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 71 through 139 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 140 through 175 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 176 through 278 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 0 through 36 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 37 through 70 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 71 through 139 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 140 through 175 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 176 through 277 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 0 through 70 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 71 through 109 )

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