PDB-5scv: Crystal Structure of Dihydrofolate Reductase from Mycobacterium t...

ID or keywords:

Entry

Database: PDB / ID: 5scv

Title

Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-889

Components

Dihydrofolate reductase

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Mycobacterium tuberculosis / DHFR / NADP / Folate / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

NADP+ binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-889
Authors: Mayclin, S.J. / Fairman, J.W. / Dranow, D.M. / Conrady, D.G. / Fox III, D. / Lukacs, C.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. / Abendroth, J.

History

Deposition	Dec 20, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 9, 2022	Provider: repository / Type: Initial release
Revision 1.1	Mar 2, 2022	Group: Other / Structure summary Category: pdbx_SG_project / pdbx_database_status / struct_keywords Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.2	May 22, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5scv.cif.gz	157.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5scv.ent.gz	123.7 KB	Display	PDB format
PDBx/mmJSON format	5scv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5scv_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	5scv_full_validation.pdf.gz	1.5 MB	Display
Data in XML	5scv_validation.xml.gz	20 KB	Display
Data in CIF	5scv_validation.cif.gz	28.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sc/5scv ftp://data.pdbj.org/pub/pdb/validation_reports/sc/5scv	HTTPS FTP

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Group deposition

ID	G_1002223 (26 entries) 5scm 5scn 5sco 5scp 5scq 5scr 5scs 5sct 5scu 5scv
Title	DHFR structures, SSGCID
Type	ground state
Description	human and M. tuberculosis DHFR structures bound to ligands

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Related structure data

Similar structure data	4xzd-1 4jet-9 4y1q-3 4jet-3 4y1q-8 1oh4-d 4jet-1 4jet-2 4y1q-5 4jes-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (8)

Deposited unit

A: Dihydrofolate reductase

B: Dihydrofolate reductase

hetero molecules

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

1

A: Dihydrofolate reductase

hetero molecules

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

2

B: Dihydrofolate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	30.260, 67.420, 75.250
Angle α, β, γ (deg.)	90.000, 96.420, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

biological unit is a monomer

#1: Protein	Dihydrofolate reductase Mass: 19832.365 Da / Num. of mol.: 2 / Fragment: MtDHFR Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: ATCC 25618 / H37Rv / Gene: folA, dfrA, Rv2763c, MTV002.28c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WNX1, dihydrofolate reductase
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Chemical	ChemComp-H4U / 6-ethyl-5-(4-{3-[3-(1H-tetrazol-5-yl)propyl]phenoxy}butoxy)pyrimidine-2,4-diamine Mass: 412.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₂₈N₈O₂ / Feature type: SUBJECT OF INVESTIGATION
#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.: 320 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 1.92 Å³/Da / Density % sol: 36.04 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: MCSG1 F3 (267577f3): 20%PEG3350, 200mM Ammonium citrate dibasic pH5.0, 3.5mM EBSI5603, protein concentration 40.69mg/mL, cryo 20% EG, puck iri2-1

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source: Rotating Copper Anode / Type: FRE+ Superbright / Wavelength: 1.5418 Å

Detector

Type: Saturn 944+ / Detector: CCD / Date: Dec 16, 2015

Radiation

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

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 42503 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 21.442 Å² / R_merge F obs: 1 / R_merge(I) obs: 0.054 / R_rim(I) all: 0.057 / Net I/σ(I): 27.81 / Num. measured all: 410403

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
1.55-1.59		0.76	0.544	2.46	10445	3281	2815	0.63	85.8
1.59-1.63		0.878	0.533	3.55	17931	3071	2850	0.578	92.8
1.63-1.68		0.914	0.467	4.2	19669	3106	2850	0.503	91.8
1.68-1.73		0.944	0.392	5.16	19877	2919	2832	0.422	97
1.73-1.79		0.961	0.335	6.24	20227	2880	2767	0.36	96.1
1.79-1.85		0.981	0.235	8.82	20451	2768	2748	0.252	99.3
1.85-1.92		0.988	0.197	11.03	20658	2672	2663	0.21	99.7
1.92-2		0.994	0.143	15.45	21180	2595	2596	0.153	100
2-2.09		0.995	0.129	18.48	20646	2449	2444	0.137	99.8
2.09-2.19		0.997	0.101	23.85	21306	2388	2387	0.108	100
2.19-2.31		0.997	0.088	28.66	22445	2272	2266	0.093	99.7
2.31-2.45		0.998	0.077	34.08	23692	2121	2122	0.08	100
2.45-2.62		0.999	0.066	39.73	23895	2006	2004	0.069	99.9
2.62-2.83		0.999	0.058	45.75	24039	1886	1886	0.061	100
2.83-3.1		0.999	0.047	58.35	24105	1708	1707	0.048	99.9
3.1-3.47		1	0.038	77.98	27033	1574	1574	0.039	100
3.47-4		1	0.032	95.9	25303	1375	1375	0.033	100
4-4.9		1	0.027	107.79	21899	1182	1185	0.028	100
4.9-6.93		1	0.031	94.89	16738	915	912	0.032	99.7
	6.93	1	0.029	103.07	8864	524	520	0.03	99.2

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	dev_2196	refinement
PDB_EXTRACT	3.11	data extraction
PHENIX		model building
Coot		model building
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.55→37.389 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.08 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1923	2049	4.82 %
R_work	0.1602	40428	-
obs	0.1617	42477	97.28 %

Solvent computation

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

Displacement parameters

B_iso max: 77.08 Å² / B_iso mean: 19.8138 Å² / B_iso min: 6.03 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→37.389 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2597	0	158	320	3075

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2903
X-RAY DIFFRACTION	f_angle_d	1.012	3984
X-RAY DIFFRACTION	f_chiral_restr	0.056	422
X-RAY DIFFRACTION	f_plane_restr	0.005	501
X-RAY DIFFRACTION	f_dihedral_angle_d	19.179	1660

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.55-1.586	0.2726	118	0.2411	2375	2493	85
1.586-1.6257	0.2512	136	0.212	2523	2659	93
1.6257-1.6696	0.2857	129	0.2011	2546	2675	92
1.6696-1.7188	0.2246	111	0.2001	2668	2779	96
1.7188-1.7742	0.2647	141	0.1919	2649	2790	96
1.7742-1.8377	0.2293	153	0.179	2667	2820	99
1.8377-1.9112	0.2164	127	0.173	2787	2914	99
1.9112-1.9982	0.1981	146	0.1581	2747	2893	100
1.9982-2.1035	0.1931	137	0.162	2772	2909	100
2.1035-2.2353	0.1818	140	0.156	2743	2883	100
2.2353-2.4079	0.2089	148	0.1615	2762	2910	100
2.4079-2.6501	0.2154	153	0.1666	2763	2916	100
2.6501-3.0335	0.1712	119	0.1612	2814	2933	100
3.0335-3.8213	0.1739	130	0.1379	2797	2927	100
3.8213-37.4001	0.1455	161	0.1344	2815	2976	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	1.6904	-0.3794	-0.0579	2.1199	0.2397	2.3845	0.0673	0.1949	-0.2723	-0.209	-0.0235	0.0316	0.5314	0.0796	-0.0374	0.1577	0.0195	-0.001	0.1217	-0.0341	0.1388	-1.6118	-14.6037	26.0021
2	1.2842	-0.382	0.4858	0.5872	-0.4574	2.0728	-0.0194	0.1435	0.0565	-0.0202	-0.026	-0.0661	-0.1167	0.1293	0.0342	0.0515	-0.0169	0.0106	0.0958	-0.0041	0.1203	0.2749	0.4993	23.9763
3	1.772	-0.0056	1.089	0.7889	0.0393	1.7291	0.0441	-0.0827	-0.1507	0.0689	0.0157	0.0063	0.0402	-0.043	-0.0611	0.0606	0.0059	0.0202	0.0803	0.0012	0.1114	-0.9385	-9.9357	35.363
4	2.0064	1.7717	2.3283	4.0684	4.2541	6.1832	0.0551	-0.0714	0.2325	0.1747	-0.0976	-0.001	-0.0457	-0.0374	0.0672	0.0887	-0.0125	0.0143	0.0886	-0.0041	0.1245	10.1362	-23.8887	14.7189
5	3.1943	0.0192	0.3695	0.5478	0.2468	2.086	0.1442	0.2768	-0.2149	0.0056	0.0141	-0.0929	0.3195	0.2854	-0.1103	0.1211	0.0279	-0.0027	0.1377	-0.0011	0.1067	11.8571	-34.9274	1.4114
6	3.9435	0.7113	-0.1509	5.7536	1.0619	3.9233	0.0423	0.1411	0.0305	-0.0607	0.0173	0.2057	0.5748	0.2023	0.0098	0.1575	0.0061	-0.0288	0.1365	0.0067	0.0587	12.9366	-38.1267	14.6094
7	5.3027	1.3741	-0.6107	2.6259	-0.5834	2.0819	0.0002	0.141	-0.3424	-0.3219	0.0058	-0.2533	0.6938	0.2327	0.0126	0.2674	0.0546	0.0111	0.1722	0.0143	0.1339	15.4121	-42.239	17.6841
8	3.2746	3.118	-0.4685	3.0112	-0.6982	1.6327	0.0136	-0.1081	0.326	0.1528	0.1828	0.4916	-0.1243	-0.0728	-0.1898	0.17	-0.0022	-0.0202	0.1566	0.0315	0.177	9.8437	-33.0959	24.7332
9	3.1392	0.0589	-0.8967	6.6427	0.4546	4.9355	0.1268	-0.2381	0.0841	0.0852	-0.0147	0.0321	-0.089	-0.3195	-0.0559	0.0688	-0.0016	-0.0043	0.1202	0.0258	0.0611	5.8273	-30.6526	15.184
10	2.8201	-0.7296	-1.0325	6.628	5.6875	7.5849	0.0153	-0.0389	0.1791	-0.0696	-0.0048	0.0147	-0.3437	-0.1028	0.026	0.0514	-0.0022	0.0032	0.0716	-0.002	0.1005	7.9156	-24.9048	5.8043
11	2.8504	0.1598	-0.8601	0.1106	-0.5463	4.052	0.0276	-0.0011	0.1321	-0.2003	0.0567	0.0592	0.0154	-0.3865	-0.0599	0.0883	-0.0008	-0.0125	0.1249	0.0111	0.1277	-0.4742	-30.0027	2.2858
12	2.6329	-4.8921	-1.774	9.3345	4.2966	7.2398	0.1519	0.1554	0.0828	-0.1024	-0.0055	-0.1799	-0.337	0.2101	-0.1005	0.104	0.0023	0.0225	0.158	0.0048	0.1029	12.5044	-27.5141	-9.8997
13	6.5644	-3.287	-5.1754	3.3626	3.9419	5.528	0.0564	-0.1662	0.4316	0.0067	0.0446	0.0648	-0.4874	-0.0339	-0.1177	0.2017	0.0299	0.0194	0.1135	0.0086	0.1647	6.6836	-21.0665	4.4717

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -7 through 9 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 89 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 90 through 159 )	A
4	X-RAY DIFFRACTION	4	chain 'B' and (resid -6 through 9 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 35 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 36 through 49 )	B
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 50 through 76 )	B
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 77 through 89 )	B
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 90 through 106 )	B
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 107 through 115 )	B
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 116 through 139 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 140 through 150 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 151 through 159 )	B

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