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

ID or keywords:

Entry

Database: PDB / ID: 5scp

Title

Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-23

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: 1.8 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-23
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	5scp.cif.gz	155.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5scp.ent.gz	121.5 KB	Display	PDB format
PDBx/mmJSON format	5scp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5scp_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	5scp_full_validation.pdf.gz	1.4 MB	Display
Data in XML	5scp_validation.xml.gz	19.1 KB	Display
Data in CIF	5scp_validation.cif.gz	26.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sc/5scp ftp://data.pdbj.org/pub/pdb/validation_reports/sc/5scp	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	6dds-4 3r33-d 6nni-1 5sco-d 5scp-2 5scz-d 4km0-2 6dds-2 4kne-2 6nnh-2 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)	30.170, 66.680, 75.030
Angle α, β, γ (deg.)	90.000, 96.540, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Details

biological unit is a monomer, the same as asu

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Protein , 1 types, 2 molecules AB

#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

#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

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Non-polymers , 5 types, 297 molecules

#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Chemical	ChemComp-GWL / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanamide Mass: 359.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₂₅N₅O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 1.89 Å³/Da / Density % sol: 34.93 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop Details: PACT C1: 20% PEG 1500, PCB Buffer (0.1 M sodium propionate, 0.05 M sodium cacocylate, 0.1 M BIS-TRIS Propane) pH 4.00

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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: May 13, 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: 1.8→50 Å / Num. obs: 27011 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 21.337 Å² / R_merge F obs: 1 / R_merge(I) obs: 0.05 / R_rim(I) all: 0.052 / Net I/σ(I): 33.24 / Num. measured all: 273168

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
1.8-1.85		0.966	0.277	6.73	11795	2010	1859	0.3	92.5
1.85-1.9		0.976	0.259	7.3	12013	1989	1859	0.28	93.5
1.9-1.95		0.986	0.186	10.25	12274	1908	1825	0.201	95.6
1.95-2.01		0.99	0.155	12.32	12245	1887	1836	0.167	97.3
2.01-2.08		0.991	0.136	13.96	12129	1761	1739	0.147	98.8
2.08-2.15		0.994	0.111	18.34	14050	1806	1799	0.119	99.6
2.15-2.23		0.995	0.106	21.3	14763	1639	1631	0.113	99.5
2.23-2.32		0.997	0.09	25.74	15792	1643	1631	0.095	99.3
2.32-2.43		0.997	0.085	26.44	15578	1540	1542	0.09	100
2.43-2.55		0.998	0.071	31.53	16166	1505	1498	0.075	99.5
2.55-2.68		0.999	0.065	35.32	16689	1424	1422	0.068	99.9
2.68-2.85		0.999	0.058	42.49	18102	1323	1320	0.061	99.8
2.85-3.04		0.999	0.052	49.7	18998	1290	1291	0.054	100
3.04-3.29		1	0.04	60.61	17200	1174	1173	0.041	99.9
3.29-3.6		1	0.035	69.59	15517	1072	1071	0.036	99.9
3.6-4.02		1	0.031	79.88	14213	1000	1000	0.032	100
4.02-4.65		1	0.028	88.69	12125	862	860	0.029	99.8
4.65-5.69		1	0.028	84.11	10751	746	746	0.029	100
5.69-8.05		1	0.032	74.59	8435	583	584	0.033	100
	8.05	1	0.025	91.65	4333	330	325	0.025	98.5

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	dev_1932	refinement
PDB_EXTRACT	3.11	data extraction
PHENIX		model building
Coot		model building
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.8→37.271 Å / Occupancy max: 1 / Occupancy min: 0.22 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.56 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.199	1350	5 %
R_work	0.1516	25641	-
obs	0.1539	26991	98.23 %

Solvent computation

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

Displacement parameters

B_iso max: 57.35 Å² / B_iso mean: 17.6265 Å² / B_iso min: 4.71 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→37.271 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2560	0	157	290	3007

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	2811
X-RAY DIFFRACTION	f_angle_d	1.462	3846
X-RAY DIFFRACTION	f_chiral_restr	0.07	407
X-RAY DIFFRACTION	f_plane_restr	0.007	484
X-RAY DIFFRACTION	f_dihedral_angle_d	19.581	1028

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.8-1.8643	0.2334	127	0.1839	2402	2529	92
1.8643-1.939	0.2235	128	0.1706	2440	2568	95
1.939-2.0272	0.2164	133	0.1529	2540	2673	97
2.0272-2.1341	0.2129	136	0.1553	2583	2719	99
2.1341-2.2678	0.1984	136	0.1541	2579	2715	100
2.2678-2.4428	0.2168	137	0.1604	2601	2738	100
2.4428-2.6886	0.2212	137	0.1615	2598	2735	100
2.6886-3.0775	0.2096	138	0.158	2606	2744	100
3.0775-3.8766	0.1827	137	0.1383	2623	2760	100
3.8766-37.2787	0.1623	141	0.1373	2669	2810	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	1.3306	-0.7686	-0.2151	1.8648	-0.546	1.6335	0.0592	0.1298	-0.2478	-0.2633	-0.0971	-0.0097	0.4692	-0.0683	-0.0174	0.1567	0.0048	0.0187	0.0973	-0.0138	0.1469	-1.2895	-14.4121	26.7239
2	2.0263	-0.2451	-0.5343	0.5685	0.2012	2.8402	0.0265	-0.0197	-0.018	0.0076	-0.0178	-0.0293	0.0419	0.081	-0.0174	0.0364	-0.0119	-0.0131	0.0441	0.0102	0.0874	5.2277	-2.2279	33.9296
3	4.0441	-0.9726	-0.0331	3.9048	-0.2911	1.6813	-0.08	-0.1132	0.0069	0.1393	0.1202	0.0376	0.0039	0.2547	-0.0288	0.043	0.0093	-0.012	0.0916	-0.0001	0.0423	-0.9049	1.402	22.4257
4	4.0136	1.0436	0.1349	1.2698	-0.0813	1.9478	-0.041	-0.3567	0.6458	0.1087	0.032	0.019	-0.1896	0.1816	-0.0313	-0.0179	-0.0137	-0.0038	0.296	-0.0487	0.2559	6.9303	4.305	21.0317
5	5.9979	-2.6675	-0.5897	4.2781	0.9009	3.7954	0.0686	0.1688	0.3324	0.0048	-0.0223	-0.1362	-0.1983	-0.1011	-0.0124	0.0622	-0.0201	0.0053	0.1042	-0.0053	0.0849	-5.5481	6.4428	16.8522
6	0.865	0.3428	-0.1177	2.6082	-1.4068	1.5138	-0.0718	0.1009	-0.1159	-0.1028	0.0627	-0.0103	0.126	0.0245	-0.0247	0.0617	0.0198	0.0032	0.0997	-0.0197	0.096	-8.0826	-5.1436	21.5758
7	6.7169	3.5684	5.8782	4.779	3.3726	5.522	0.1733	0.0293	-0.1486	0.0919	-0.1367	-0.0629	0.1111	-0.0829	-0.0103	0.0562	0.0012	0.0129	0.0631	0.0121	0.1141	-0.3333	-11.9201	32.4215
8	8.4711	-6.9012	3.6966	7.1764	-3.7949	2.2227	-0.2921	-0.3234	0.2849	0.636	0.1636	0.0998	-0.3823	0.0791	0.098	0.1719	0.0206	-0.0172	0.1319	-0.0308	0.1515	-2.6903	1.3766	44.8054
9	2.1379	0.2741	1.5163	1.4205	-0.075	1.7319	0.0354	-0.0193	-0.3224	0.0459	0.0213	-0.0592	0.0709	0.0212	-0.0333	0.082	-0.013	0.0256	0.0733	0.0108	0.1092	2.3626	-12.3061	38.9002
10	7.7062	2.7464	6.284	2.2926	3.091	5.9225	0.41	-0.3959	-0.3324	0.2585	-0.2731	0.1017	0.4645	-0.525	-0.1714	0.1286	-0.0003	-0.0157	0.0919	0.0152	0.136	0.0961	-15.9094	34.2258
11	2.1978	1.1839	1.815	3.2367	2.4371	3.8794	0.0365	-0.1142	0.2355	0.0758	-0.076	-0.0149	-0.1981	-0.0867	0.0837	0.0967	-0.0149	0.0239	0.0834	-0.0136	0.095	10.0345	-23.5619	14.6948
12	5.5621	0.2656	-1.2292	4.2281	-1.5612	2.9377	0.1045	0.3611	-0.3913	-0.132	-0.1096	-0.0809	0.5122	0.0299	0.0218	0.1791	0.0062	-0.0157	0.1076	-0.0305	0.0971	6.2216	-37.7624	-0.7176
13	0.2487	0.4956	0.343	1.083	0.2934	2.2797	0.1312	0.2888	0.0055	-0.1299	-0.0615	-0.2459	-0.0256	0.2281	-0.0785	0.071	0.02	0.0339	0.2193	0.0211	0.129	18.4753	-29.9916	3.8485
14	3.1379	1.1579	-0.2911	2.6126	-0.5965	2.7737	-0.0816	0.0576	-0.2665	-0.1827	0.0516	-0.1483	0.4757	0.2442	0.03	0.1417	0.0256	0.0074	0.1036	-0.0042	0.1145	14.5441	-40.3289	16.602
15	0.6406	1.1711	-0.4305	6.862	-1.5221	1.2791	-0.1599	0.031	0.142	0.3728	0.2893	0.2495	-0.1811	0.0383	-0.1169	0.1491	0.0095	0.0105	0.1306	0.0079	0.1116	10.0253	-32.6958	24.7049
16	2.2852	-0.0599	-0.0405	3.698	0.5229	3.8477	0.1387	-0.3294	0.0713	0.1171	-0.0565	0.0187	-0.2384	-0.3127	-0.0361	0.0836	-0.0024	0.0026	0.1176	0.0038	0.0559	5.7408	-30.2376	15.1344
17	2.5282	-0.719	-0.8383	3.7802	2.2231	2.0867	0.1015	0.0826	0.2511	-0.0802	0.0726	-0.1102	-0.3325	0.0723	-0.115	0.0761	-0.001	0.0127	0.0836	0.0126	0.0914	7.9165	-24.384	5.8307
18	4.7559	2.1523	-2.9537	1.1132	-1.7865	3.3313	-0.1407	0.2441	-0.4109	-0.2973	0.143	-0.1235	0.6154	-0.2861	-0.0002	0.1636	-0.0611	-0.0412	0.1264	0.0046	0.1254	-1.3486	-36.9365	-2.9405
19	2.778	1.6914	0.435	1.9976	-1.3316	3.6067	0.1059	-0.0147	0.6336	-0.2603	-0.0682	-0.0841	-0.6958	-0.3114	0.016	0.1813	0.041	0.0337	0.1317	-0.0073	0.2327	0.0824	-22.8387	6.7982
20	2.5578	1.3238	-0.7939	3.4715	1.5575	6.7634	0.0901	0.0185	-0.1386	0.1298	-0.084	-0.0889	-0.1989	0.1769	0.0522	0.089	0.0084	0.0008	0.1054	0.024	0.0978	13.2726	-27.258	-9.6108
21	1.3402	-0.5815	-0.4501	2.0886	1.9406	1.8181	0.0296	0.017	0.1487	0.187	-0.1123	0.293	-0.4759	-0.2283	0.1899	0.2653	0.0399	0.0288	0.1037	0.0069	0.1493	7.1069	-20.8569	3.3704

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -8 through 9 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 35 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 36 through 49 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 50 through 60 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 61 through 76 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 77 through 106 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 107 through 115 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 116 through 125 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 126 through 150 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 151 through 159 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -6 through 9 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 10 through 24 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 25 through 35 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 36 through 76 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 77 through 89 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 90 through 106 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 107 through 115 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 116 through 125 )	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 126 through 139 )	B
20	X-RAY DIFFRACTION	20	chain 'B' and (resid 140 through 150 )	B
21	X-RAY DIFFRACTION	21	chain 'B' and (resid 151 through 159 )	B

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 297 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Open data

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Validation report

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Assembly

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Components

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Protein , 1 types, 2 molecules AB

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Non-polymers , 5 types, 297 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Yorodumi