PDB-7km8: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact...

ID or keywords:

Entry

Database: PDB / ID: 7km8

Title

Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, orthorhombic crystal from

Components

Dihydrofolate reductase

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SSGCID / SDDC / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

dihydrofolate metabolic process / glycine biosynthetic 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 ulcerans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.55 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001914, orthorhombic crystal form
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Nov 2, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 7, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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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Download

PDBx/mmCIF format	7km8.cif.gz	190.6 KB	Display	PDBx/mmCIF format
PDB format	pdb7km8.ent.gz	122.9 KB	Display	PDB format
PDBx/mmJSON format	7km8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7km8_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	7km8_full_validation.pdf.gz	1.6 MB	Display
Data in XML	7km8_validation.xml.gz	20.8 KB	Display
Data in CIF	7km8_validation.cif.gz	31.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/km/7km8 ftp://data.pdbj.org/pub/pdb/validation_reports/km/7km8	HTTPS FTP

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Related structure data

Related structure data	6uwwS S: Starting model for refinement
Similar structure data	6nni-2 6vs8-2 7km8-2 6vs9-1 5zj5-2 6vv8-2 6vv6-1 3sh2-2 6ddp-1 7d4x-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
Other databases	TargetTrack: SSGCID-MyulA.01062.a.B13

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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

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

1

A: Dihydrofolate reductase

hetero molecules

defined by author
Evidence: gel filtration
20.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Dihydrofolate reductase

hetero molecules

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

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	78.030, 82.790, 133.120
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	24
Space group name H-M	I2₁2₁2₁
Space group name Hall	I2b2c
Symmetry operation	#1: x,y,z #2: x,-y,-z+1/2 #3: -x+1/2,y,-z #4: -x,-y+1/2,z #5: x+1/2,y+1/2,z+1/2 #6: x+1/2,-y+1/2,-z+1 #7: -x+1,y+1/2,-z+1/2 #8: -x+1/2,-y+1,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	A-539- HOH
2	1	A-552- HOH
3	1	B-528- HOH

#1: Protein	Dihydrofolate reductase Mass: 19035.619 Da / Num. of mol.: 2 / Mutation: C89S, E96A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria) Strain: Agy99 / Gene: dfrA, MUL_2179 / Plasmid: MyulA.01062.a.B13 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0PQG8, 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-WPD / (2S)-2-[(3-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)methyl]-3,3-difluoropropanoic acid Mass: 410.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₉H₂₄F₂N₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 523 / 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: 2.83 Å³/Da / Density % sol: 56.5 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus screen condition a9: 10% (w/V) PEG 20,000, 20% (V/V) PEG MME 550: 30mM each magnesium chloride, calcium chloride: 100m bicine / trizma base HCl pH 7.5: MyulA.01062.a.B13.PS38588 at ...Details: Morpheus screen condition a9: 10% (w/V) PEG 20,000, 20% (V/V) PEG MME 550: 30mM each magnesium chloride, calcium chloride: 100m bicine / trizma base HCl pH 7.5: MyulA.01062.a.B13.PS38588 at 7.98mg/mll + 2.5 mM NADP and SDDC-0001914 (bsi111353): tray 318487a9: cryo: direct: puck poq5-9

Crystal

Density Matthews: 2.83 Å³/Da / Density % sol: 56.5 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Morpheus screen condition a9: 10% (w/V) PEG 20,000, 20% (V/V) PEG MME 550: 30mM each magnesium chloride, calcium chloride: 100m bicine / trizma base HCl pH 7.5: MyulA.01062.a.B13.PS38588 at ...

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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: Oct 22, 2020

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.55→50 Å / Num. obs: 62683 / % possible obs: 99.9 % / Redundancy: 6.121 % / B_iso Wilson estimate: 22.779 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.069 / Χ²: 0.928 / Net I/σ(I): 17.91

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
1.55-1.59	6.093	0.583	3.24	4627	0.873	0.638	100
1.59-1.63	6.128	0.504	3.7	4439	0.898	0.552	100
1.63-1.68	6.129	0.428	4.43	4372	0.929	0.468	100
1.68-1.73	6.14	0.34	5.58	4215	0.948	0.372	100
1.73-1.79	6.14	0.271	6.88	4112	0.968	0.297	100
1.79-1.85	6.163	0.196	9.16	3978	0.983	0.215	99.9
1.85-1.92	6.143	0.163	11.2	3840	0.987	0.178	99.9
1.92-2	6.165	0.124	14.1	3698	0.992	0.136	99.9
2-2.09	6.142	0.102	16.72	3548	0.994	0.112	99.9
2.09-2.19	6.151	0.083	20.04	3398	0.996	0.091	99.9
2.19-2.31	6.146	0.076	22.2	3240	0.996	0.083	99.8
2.31-2.45	6.167	0.065	24.83	3056	0.997	0.071	100
2.45-2.62	6.153	0.054	28.71	2882	0.998	0.059	99.9
2.62-2.83	6.142	0.048	31.41	2709	0.998	0.053	99.9
2.83-3.1	6.114	0.042	35.33	2494	0.998	0.046	100
3.1-3.47	6.07	0.036	40.85	2249	0.999	0.039	99.5
3.47-4	6.073	0.032	44.87	2002	0.999	0.034	99.7
4-4.9	6.027	0.028	46.69	1714	0.999	0.031	99.6
4.9-6.93	5.96	0.03	44.85	1334	0.999	0.033	99.3
6.93-50	5.549	0.028	46.08	776	0.999	0.031	97.2

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19rc4	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NAD and P218-bound structure, PDB entry 6uww

6uww

Resolution: 1.55→39.11 Å / SU ML: 0.1298 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.9251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1778	1932	3.08 %	0
R_work	0.1561	60742	-	-
obs	0.1568	62674	99.86 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 20.91 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→39.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2428	0	158	523	3109

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	2739
X-RAY DIFFRACTION	f_angle_d	0.9764	3769
X-RAY DIFFRACTION	f_chiral_restr	0.0607	417
X-RAY DIFFRACTION	f_plane_restr	0.0089	513
X-RAY DIFFRACTION	f_dihedral_angle_d	13.5725	1043

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 (%)
1.55-1.59	0.2197	150	0.193	4298	X-RAY DIFFRACTION	100
1.59-1.63	0.2143	136	0.1865	4273	X-RAY DIFFRACTION	99.98
1.63-1.68	0.2091	143	0.1793	4325	X-RAY DIFFRACTION	100
1.68-1.73	0.203	118	0.1733	4285	X-RAY DIFFRACTION	100
1.73-1.8	0.2141	145	0.1859	4319	X-RAY DIFFRACTION	99.96
1.8-1.87	0.1928	154	0.1686	4287	X-RAY DIFFRACTION	99.95
1.87-1.95	0.2068	151	0.1614	4293	X-RAY DIFFRACTION	99.91
1.95-2.06	0.1853	160	0.1605	4297	X-RAY DIFFRACTION	99.89
2.06-2.18	0.1819	148	0.1642	4329	X-RAY DIFFRACTION	99.93
2.18-2.35	0.1726	108	0.1567	4346	X-RAY DIFFRACTION	99.87
2.35-2.59	0.1709	110	0.1558	4387	X-RAY DIFFRACTION	99.93
2.59-2.96	0.1649	137	0.159	4360	X-RAY DIFFRACTION	99.87
2.96-3.73	0.1772	127	0.144	4410	X-RAY DIFFRACTION	99.65
3.73-39.11	0.148	145	0.1369	4533	X-RAY DIFFRACTION	99.15

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	1.88767686231	-0.873174729465	-0.252479726906	2.92730187395	0.311556777593	4.29216724767	0.0617141364565	0.124783234631	0.0104505610836	-0.219958912965	-0.144484828469	-0.119981917757	0.251427542475	0.51503944485	0.0630945887848	0.213929349117	0.0588638350614	0.0210281496457	0.152905354876	0.0427653062785	0.124219578215	-30.6293641981	10.6586871249	-19.2438977855
2	2.65345783871	-0.418367582939	-0.343538811161	2.80577597747	0.415917253605	2.45611540133	-0.0327125234402	0.0856782804756	-0.0943641258754	0.0234570436783	0.00518939803424	-0.00845236827415	0.0127466315713	0.000764693125398	0.00306021364041	0.051741995921	0.00560095967978	-0.0187423245474	0.100746165094	0.000545622042972	0.0700126422866	-20.100215625	-16.3388499014	-16.885146953
3	2.39515119657	-0.00913230478418	0.313638313708	3.73704139324	3.57438668673	7.15014873133	-0.0960046544711	0.166595156644	0.247481645091	-0.176657741057	0.234111862222	-0.125339606563	-0.185842104723	0.261297825534	-0.0773021612925	0.103937476832	-0.0155141095354	-0.00611173702241	0.131407657706	0.0380975523566	0.140610483718	-15.3443659653	-7.24847761931	-23.13162513
4	2.83617565433	0.571259322193	0.539484860977	2.50447250513	1.25690151849	2.88033273687	-0.0309713113808	0.173219927688	-0.114074683856	-0.104135696481	-0.0274504599665	-0.00948002406758	-0.0935338195192	0.0498662668527	0.0329253584145	0.0699510492539	0.0108534911154	-0.020413179278	0.089601679799	0.0148276350709	0.0666316932261	-24.8688202622	-16.244335652	-29.2994224083
5	3.40821863767	-3.46140434756	-3.16603435394	3.63490465389	2.81227985482	4.44941790402	0.0672028156014	0.215178765673	0.018638924024	-0.265865647833	-0.130324934997	0.220349265275	-0.433572979961	-0.164714596589	0.0410914490973	0.165223247298	0.016707014084	-0.0467102464303	0.144528706029	0.00876074693378	0.0990523292877	-27.0957807562	-8.24396465706	-29.0373514423
6	2.60688978594	2.45734142313	1.10921760274	7.73045191275	-1.14388111372	4.65698476763	0.0490581528466	0.298828072411	-0.319226440419	-0.526160728629	0.168522437569	-0.0289623289685	0.470489757645	0.178242928931	-0.157207756056	0.174253001432	0.0218661980141	-0.0325689970492	0.16501547662	-0.0295969185157	0.126484935666	-26.6339045036	-21.6995196614	-35.9562391591
7	2.79637943085	0.458611625513	0.940155279833	2.45162928293	0.941554217315	2.66719841068	0.0738369857968	0.292195074166	-0.195920661396	-0.161955009263	0.107647437516	-0.192675547241	0.0937387773033	0.221182799197	-0.19252601397	0.0912621942769	0.0191027428994	-0.00184256426061	0.126051705248	-0.00541313475065	0.102940548543	-14.6322382996	-20.9728469804	-24.8551002768
8	7.62307386611	6.19999116895	1.90735064834	5.23745307509	2.1164948894	2.4636204713	0.439964551066	-0.579344386714	-0.000681203673067	0.624270284357	-0.427622088758	0.20161168782	0.247030085813	-0.289014558147	0.0454118287867	0.170819534849	-0.0196045720563	0.00146109019196	0.19185970966	0.0240730350601	0.17865574935	-24.5469850104	-21.1033318526	-7.84298460728
9	5.05999241736	0.586866996598	-1.73816942374	0.0694716277706	-0.193040021872	0.58785016099	-0.185257827443	-0.550061456319	-0.624474022941	0.0109342346754	0.0255250658264	-0.214570061984	0.035468726973	0.22099634522	0.148199251907	0.120896222389	0.0356940251776	0.00768485910727	0.209804872331	0.0331257862012	0.247290455684	-8.73959438999	-24.5972654285	-18.0774067391
10	3.22748703375	-1.75260583285	-1.56023805351	3.08535158428	2.69807238463	4.54904656462	0.0135124710549	0.113901223778	-0.060223200057	-0.0162996808638	-0.114322532754	0.0349033961496	-0.102635176041	-0.010814929762	0.102892697398	0.0593123623976	0.00216111306229	-0.0160613756231	0.110320341777	0.000200918185734	0.0897129372712	-9.4546404758	-11.8304358307	-14.1409376924
11	2.33636427534	-0.286238557212	-0.322415213819	3.12713069818	-0.616292048641	2.16136700718	0.0640584804785	0.00696433218133	-0.041186364325	-0.270871035801	-0.0439523667639	0.181548915188	-0.0629539864394	-0.0268118038819	-0.0250144854391	0.119968473624	0.0168287618654	-0.0299531954608	0.0676185708302	0.00863512229677	0.0781201673759	-35.8131469314	0.407775496034	-15.9244763596
12	5.15616899255	-0.514183112577	-3.75481289653	2.98994057158	0.318151616366	2.74891342332	0.142323532629	-0.0254546714598	0.103669582113	-0.0201277154983	-0.0321865988511	-0.24138809237	0.088643222167	0.271031766577	-0.143532012409	0.140041977698	0.0127222089948	-0.00875053057616	0.112298134777	0.0112822012328	0.123105768093	-26.1682668014	4.28816202701	-10.1856056955
13	1.94334885906	-0.0841428211742	-0.212694918291	1.66553385456	-0.0450751467719	2.47252240596	-0.0252460221522	-0.117496104536	-0.0444598573468	0.0308475963115	0.00243729156542	8.75433393156E-5	0.021095847518	0.0516506950519	0.0126270171796	0.0798461051765	0.008607147164	-0.00660513563316	0.0851711682565	0.0175162437431	0.084312155312	-32.3924214828	-5.78245771877	-4.04239843837
14	5.96079076464	0.906444498082	0.831220036069	2.37551490132	-0.495678567725	4.40975101302	-0.0239829337755	-0.318181388027	0.0830273854213	0.128982585884	0.128041896728	0.34760116828	-0.0768569099849	-0.416690516528	-0.0514332851252	0.0743272283854	0.00776726036122	0.0134297477472	0.131477069797	0.0222984091414	0.115366883597	-41.1037715391	-6.88515392408	2.87689569593
15	2.58563644636	0.393621507397	-0.463271358867	3.45873195748	-0.664534782009	1.80779690491	0.0884901602967	0.0800330622656	0.0308935684821	-0.359143607293	-0.00356628978468	0.369291737954	-0.0679953621002	-0.14563681058	0.00659121055129	0.154605575021	0.0402412054514	-0.0488152207085	0.0989198667067	0.00545081060851	0.134251600992	-41.01826047	5.40896519749	-13.4775046505

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'B' and (resid 146 through 165 )	B	F	146 - 165	139 - 158
2	2	chain 'A' and (resid 2 through 26 )	A	A	2 - 26	1 - 25
3	3	chain 'A' and (resid 27 through 37 )	A	A	27 - 37	26 - 36
4	4	chain 'A' and (resid 38 through 51 )	A	A	38 - 51	37 - 50
5	5	chain 'A' and (resid 52 through 62 )	A	A	52 - 62	51 - 61
6	6	chain 'A' and (resid 63 through 96 )	A	A	63 - 96	62 - 89
7	7	chain 'A' and (resid 97 through 121 )	A	A	97 - 121	90 - 114
8	8	chain 'A' and (resid 122 through 131 )	A	A	122 - 131	115 - 124
9	9	chain 'A' and (resid 132 through 145 )	A	A	132 - 145	125 - 138
10	10	chain 'A' and (resid 146 through 165 )	A	A	146 - 165	139 - 158
11	11	chain 'B' and (resid 2 through 26 )	B	F	2 - 26	1 - 25
12	12	chain 'B' and (resid 27 through 37 )	B	F	27 - 37	26 - 36
13	13	chain 'B' and (resid 38 through 62 )	B	F	38 - 62	37 - 61
14	14	chain 'B' and (resid 63 through 89 )	B	F	63 - 89	62 - 88
15	15	chain 'B' and (resid 96 through 145 )	B	F	96 - 145	89 - 138

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