PDB-6omz: Crystal Structure of Dihydropteroate synthase from Mycobacterium ...

ID or keywords:

Entry

Database: PDB / ID: 6omz

Title

Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate

Components

Dihydropteroate synthase

Keywords

LIGASE / SSGCID / PMM / dihydropteroate synthase / ptp / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

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

Mycobacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Dihydropteroate synthase from Mycobacterium smegmatis with bound 6-hydroxymethylpterin-monophosphate
Authors: Bolejack, M.J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Apr 19, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 8, 2019	Provider: repository / Type: Initial release
Revision 1.1	Oct 11, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6omz.cif.gz	129.6 KB	Display	PDBx/mmCIF format
PDB format	pdb6omz.ent.gz	97.6 KB	Display	PDB format
PDBx/mmJSON format	6omz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6omz_validation.pdf.gz	664 KB	Display	wwPDB validaton report
Full document	6omz_full_validation.pdf.gz	665.5 KB	Display
Data in XML	6omz_validation.xml.gz	12.7 KB	Display
Data in CIF	6omz_validation.cif.gz	18.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/om/6omz ftp://data.pdbj.org/pub/pdb/validation_reports/om/6omz	HTTPS FTP

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Related structure data

Related structure data	1eyeS S: Starting model for refinement
Similar structure data	3rlp-2 3rlr-2 3k98-2 1osf-d 7cof-d 3vc1-4 4gx9-3 7cog-3 4lip-2 1hqd-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: Dihydropteroate synthase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	47.720, 96.410, 135.070
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-611- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase Mass: 30517.586 Da / Num. of mol.: 1 / Fragment: MysmA.01019.b.B2 / Mutation: G281E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium smegmatis (strain MKD8) (bacteria) Strain: MKD8 / Gene: D806_059810 / Variant: MKD8 / Plasmid: MysmA.01019.b.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): BL21(DE3) / References: UniProt: A0A2U9PYL8, dihydropteroate synthase

#1: Protein

Dihydropteroate synthase / DHPS / Dihydropteroate pyrophosphorylase

Mass: 30517.586 Da / Num. of mol.: 1 / Fragment: MysmA.01019.b.B2 / Mutation: G281E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycobacterium smegmatis (strain MKD8) (bacteria)
Strain: MKD8 / Gene: D806_059810 / Variant: MKD8 / Plasmid: MysmA.01019.b.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): BL21(DE3) / References: UniProt: A0A2U9PYL8, dihydropteroate synthase

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Non-polymers , 5 types, 335 molecules

#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-PMM / PTERIN-6-YL-METHYL-MONOPHOSPHATE Mass: 273.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₇H₈N₅O₅P
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.63 Å³/Da / Density % sol: 53.31 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5 Details: MysmA.01019.b.B1.PW38386 was crystallized at 14 mg/mL and 14 ??C with 2.5 mM 6-Hydroxymethylpterin-monophosphate and mixed 1:1 with a solution of 0.2 M ammonium citrate dibasic pH 5.0 and ...Details: MysmA.01019.b.B1.PW38386 was crystallized at 14 mg/mL and 14 ??C with 2.5 mM 6-Hydroxymethylpterin-monophosphate and mixed 1:1 with a solution of 0.2 M ammonium citrate dibasic pH 5.0 and 20% (w/v) PEG3350, 20% ethylene glycol cryo. Tray: 308720f3, puck: bqx9-6.

Crystal

Density Matthews: 2.63 Å³/Da / Density % sol: 53.31 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: MysmA.01019.b.B1.PW38386 was crystallized at 14 mg/mL and 14 ??C with 2.5 mM 6-Hydroxymethylpterin-monophosphate and mixed 1:1 with a solution of 0.2 M ammonium citrate dibasic pH 5.0 and ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Apr 11, 2019 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.85→32.904 Å / Num. obs: 26566 / % possible obs: 98.2 % / Redundancy: 6.907 % / B_iso Wilson estimate: 26.165 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.072 / R_rim(I) all: 0.078 / Χ²: 1.049 / Net I/σ(I): 19.72 / Num. measured all: 183484

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	5.073	0.5	3.03	8355	1959	1647	0.856	0.555	84.1
1.9-1.95	5.524	0.405	4.03	9788	1907	1772	0.906	0.446	92.9
1.95-2.01	6.522	0.341	5.65	12411	1908	1903	0.938	0.371	99.7
2.01-2.07	7.361	0.274	7.62	13419	1824	1823	0.974	0.295	99.9
2.07-2.14	7.363	0.215	9.48	12811	1740	1740	0.983	0.232	100
2.14-2.21	7.305	0.175	11.61	12499	1714	1711	0.987	0.189	99.8
2.21-2.29	7.324	0.153	13.19	12055	1646	1646	0.989	0.165	100
2.29-2.39	7.286	0.137	14.47	11651	1600	1599	0.991	0.147	99.9
2.39-2.49	7.285	0.106	18.06	11030	1514	1514	0.994	0.115	100
2.49-2.62	7.217	0.095	19.72	10630	1475	1473	0.995	0.103	99.9
2.62-2.76	7.261	0.084	21.8	10114	1398	1393	0.997	0.091	99.6
2.76-2.93	7.223	0.074	25.02	9506	1320	1316	0.997	0.08	99.7
2.93-3.13	7.142	0.059	30.13	8885	1248	1244	0.998	0.064	99.7
3.13-3.38	7.089	0.046	35.69	8365	1183	1180	0.998	0.05	99.7
3.38-3.7	7.128	0.041	39.78	7549	1064	1059	0.999	0.044	99.5
3.7-4.14	6.991	0.036	44.1	6949	997	994	0.999	0.039	99.7
4.14-4.78	7.045	0.031	47.22	6136	872	871	0.999	0.033	99.9
4.78-5.85	6.999	0.032	45.9	5186	742	741	0.999	0.034	99.9
5.85-8.27	6.795	0.028	46.02	4002	589	589	0.999	0.031	100
8.27-32.904	6.105	0.025	52.58	2143	356	351	0.999	0.027	98.6

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	(1.15.2_3472: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1EYE

1eye

Resolution: 1.85→32.904 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.78 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1861	2094	7.89 %	RANDOM, 0
R_work	0.1509	-	-	-
obs	0.1537	26556	98.18 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.85→32.904 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1996	0	80	323	2399

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2145
X-RAY DIFFRACTION	f_angle_d	0.806	2927
X-RAY DIFFRACTION	f_dihedral_angle_d	13.696	1273
X-RAY DIFFRACTION	f_chiral_restr	0.058	336
X-RAY DIFFRACTION	f_plane_restr	0.005	402

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 (%)
1.8501-1.8931	0.2547	120	0.2207	1355	X-RAY DIFFRACTION	84
1.8931-1.9404	0.271	123	0.1986	1497	X-RAY DIFFRACTION	92
1.9404-1.9929	0.2336	155	0.1776	1653	X-RAY DIFFRACTION	99
1.9929-2.0515	0.2364	117	0.1773	1632	X-RAY DIFFRACTION	100
2.0515-2.1177	0.1984	136	0.1687	1630	X-RAY DIFFRACTION	100
2.1177-2.1934	0.209	144	0.1583	1636	X-RAY DIFFRACTION	100
2.1934-2.2812	0.1846	157	0.1524	1630	X-RAY DIFFRACTION	100
2.2812-2.385	0.1726	133	0.1488	1658	X-RAY DIFFRACTION	100
2.385-2.5107	0.1862	162	0.1485	1636	X-RAY DIFFRACTION	100
2.5107-2.6679	0.1889	133	0.1507	1668	X-RAY DIFFRACTION	100
2.6679-2.8738	0.2007	139	0.1546	1650	X-RAY DIFFRACTION	100
2.8738-3.1628	0.1997	143	0.1487	1678	X-RAY DIFFRACTION	100
3.1628-3.62	0.1788	123	0.1393	1680	X-RAY DIFFRACTION	100
3.62-4.5589	0.1463	145	0.1238	1693	X-RAY DIFFRACTION	100
4.5589-32.9088	0.1658	164	0.15	1766	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	2.9973	-4.7842	-2.4562	8.6139	2.1335	6.0894	0.2326	0.2924	0.3645	0.0049	-0.2384	-0.168	-0.0223	-0.2341	0.0267	0.1401	-0.0251	-0.0066	0.0639	0.0203	0.1245	-3.5409	58.443	15.2154
2	7.3448	-5.8404	-0.9406	4.7644	0.9889	1.9892	-0.0476	0.3633	-0.2398	-0.055	-0.1826	0.6632	0.0424	-0.4716	0.1605	0.1657	-0.0401	-0.0113	0.2256	-0.0253	0.2444	-14.3551	57.4546	17.6974
3	2.6281	0.932	0.0414	0.5128	0.7799	3.2272	-0.0919	-0.0307	0.4448	0.2948	0.0722	0.1138	-0.4869	-0.1888	0.0345	0.1495	0.0163	0.0441	0.1382	-0.0053	0.1603	-5.4124	66.7654	15.0968
4	4.105	-1.5345	0.047	6.0876	-1.6044	5.6065	-0.0504	-0.2127	0.1309	0.2561	0.0638	0.0839	-0.0501	-0.0481	0.0001	0.0953	0.0142	0.009	0.1334	-0.0284	0.0651	-4.3068	65.2217	25.8514
5	4.5869	-0.4977	1.3957	6.4394	0.7527	4.7735	0.0274	-0.2527	0.2075	0.1251	-0.0265	0.0307	-0.2608	0.2161	0.0168	0.0746	-0.0143	0.0154	0.1291	-0.0067	0.0858	6.9407	69.6065	23.0892
6	3.8893	1.0118	-0.0476	0.2819	-0.2161	1.5535	0.0346	-0.1209	0.7316	0.0146	0.0339	-0.1107	-0.3638	-0.1426	-0.0886	0.2211	0.0152	0.0328	0.1279	0.0126	0.2371	6.9752	78.4982	3.8879
7	0.8562	0.4583	-0.2479	1.9548	0.6171	1.4229	-0.003	-0.0133	0.007	-0.0777	0.0734	-0.0267	-0.0356	0.0695	-0.0702	0.071	0.0086	0.0013	0.095	0.0022	0.0839	8.7105	62.7227	6.4108
8	6.0607	-1.8255	-1.1453	3.2689	1.0624	1.2698	-0.0885	-0.3041	-0.2427	0.2089	0.1971	-0.0462	0.3564	0.1516	-0.1439	0.1993	0.0087	-0.0177	0.098	-0.0021	0.0877	9.0261	40.8009	7.3159

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 12 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 48 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 49 through 69 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 70 through 107 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 108 through 138 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 139 through 156 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 157 through 264 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 265 through 285 )

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