PDB-7k62: Crystal Structure of Dihydrofolate reductase from Mycobacterium k...

ID or keywords:

Entry

Database: PDB / ID: 7k62

Title

Crystal Structure of Dihydrofolate reductase from Mycobacterium kansasii in complex with NADP and inhibitor P218

Components

Dihydrofolate reductase

Keywords

OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SSGCID / tetrahydrofolate biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex

Function / homology

Function and homology information

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

Biological species

Mycobacterium kansasii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To Be Published
Title: Crystal Structure of Dihydrofolate reductase from Mycobacterium kansasii in complex with NADP and inhibitor P218
Authors: Abendroth, J. / Dranow, D.M. / Santhakumar, V. / Walpole, C. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Sep 18, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 17, 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	7k62.cif.gz	185.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7k62.ent.gz	122 KB	Display	PDB format
PDBx/mmJSON format	7k62.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k6/7k62 ftp://data.pdbj.org/pub/pdb/validation_reports/k6/7k62	HTTPS FTP

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Related structure data

Related structure data	1df7S S: Starting model for refinement
Similar structure data	6vs9-2 3qyo-d 6nni-1 4qle-2 6yl9-2 5eaj-1 3och-2 6nni-2 6dds-3 4qbk-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-MykaA.01062.a

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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

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

1

A: Dihydrofolate reductase

hetero molecules

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

2

B: Dihydrofolate reductase

hetero molecules

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

Unit cell

Length a, b, c (Å)	62.100, 66.250, 86.120
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein	Dihydrofolate reductase Mass: 18737.018 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: B / Source: (gene. exp.) Mycobacterium kansasii (bacteria) / Gene: folA, BZL29_1474, BZL30_0350 / Plasmid: MykaA.01062.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1V3XYG5, 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid Mass: 360.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₈H₂₄N₄O₄ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.38 Å³/Da / Density % sol: 48.3 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Microlytics Morpheus screen, condition E4: 12.5% (w/V) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (V/V) MPD: 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, ...Details: Microlytics Morpheus screen, condition E4: 12.5% (w/V) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (V/V) MPD: 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, pentaethyleneglycol: 100mM MES/imidazole pH 6.5. MykaA.01062.a.B1.PS38569 at 5.22mg/ml + 2mM each NADP and P218: tray 309622 e4: cryo: direct: puck kdu7-7

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48.3 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Microlytics Morpheus screen, condition E4: 12.5% (w/V) PEG 1000, 12.5% (w/v) PEG 3350, 12.5% (V/V) MPD: 30mM of each diethyleneglycol, triethyleneglycol, tetraethyleneglycol, ...

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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: Aug 6, 2020 / 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: 2.05→50 Å / Num. obs: 22844 / % possible obs: 99.7 % / Redundancy: 5.108 % / B_iso Wilson estimate: 42.831 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.06 / R_rim(I) all: 0.067 / Χ²: 0.884 / Net I/σ(I): 14.45

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
2.05-2.1	3.947	0.598	1.99	1637	0.826	0.692	99.3
2.1-2.16	4.854	0.51	2.77	1625	0.94	0.574	99.4
2.16-2.22	5.304	0.469	3.27	1586	0.948	0.522	99.9
2.22-2.29	5.307	0.356	4.16	1522	0.97	0.396	99.9
2.29-2.37	5.288	0.324	4.49	1495	0.977	0.36	99.7
2.37-2.45	5.299	0.247	5.6	1435	0.989	0.275	99.9
2.45-2.54	5.301	0.221	6.28	1397	0.988	0.246	99.9
2.54-2.65	5.293	0.186	7.38	1333	0.992	0.207	99.6
2.65-2.76	5.278	0.13	9.68	1298	0.998	0.144	99.8
2.76-2.9	5.25	0.108	11.65	1226	0.997	0.12	99.9
2.9-3.06	5.252	0.077	15.34	1189	0.999	0.086	99.7
3.06-3.24	5.25	0.063	19.44	1118	0.998	0.07	99.8
3.24-3.47	5.226	0.047	25.39	1069	0.999	0.052	99.9
3.47-3.74	5.191	0.037	30.99	986	0.999	0.041	100
3.74-4.1	5.193	0.033	35.77	916	0.999	0.036	99.6
4.1-4.58	5.133	0.029	38.82	825	0.999	0.032	99.9
4.58-5.29	5.087	0.028	39.18	743	1	0.031	99.6
5.29-6.48	5.038	0.028	38.27	639	0.999	0.031	99.7
6.48-9.17	4.864	0.022	42.15	509	1	0.025	100
9.17-50	4.361	0.021	44.62	296	0.999	0.024	97

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18.2	refinement
PDB_EXTRACT	3.25	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 1df7 as per Morda

1df7

Resolution: 2.05→35.39 Å / SU ML: 0.3333 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.7307
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2683	1978	8.72 %	0
R_work	0.2109	20698	-	-
obs	0.216	22676	99 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 51.07 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→35.39 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2597	0	156	94	2847

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	2852
X-RAY DIFFRACTION	f_angle_d	0.9194	3904
X-RAY DIFFRACTION	f_chiral_restr	0.052	402
X-RAY DIFFRACTION	f_plane_restr	0.0095	542
X-RAY DIFFRACTION	f_dihedral_angle_d	15.9948	1070

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 (%)
2.05-2.1	0.4326	139	0.3598	1430	X-RAY DIFFRACTION	98.99
2.1-2.16	0.3603	139	0.3293	1452	X-RAY DIFFRACTION	98.27
2.16-2.22	0.3513	150	0.2963	1449	X-RAY DIFFRACTION	99.01
2.22-2.29	0.3843	133	0.2771	1448	X-RAY DIFFRACTION	98.94
2.29-2.38	0.3859	123	0.2758	1465	X-RAY DIFFRACTION	98.69
2.38-2.47	0.413	128	0.2781	1479	X-RAY DIFFRACTION	98.29
2.47-2.58	0.357	154	0.2813	1438	X-RAY DIFFRACTION	98.94
2.58-2.72	0.3715	127	0.2738	1486	X-RAY DIFFRACTION	98.84
2.72-2.89	0.339	153	0.2638	1454	X-RAY DIFFRACTION	99.14
2.89-3.11	0.293	141	0.2295	1480	X-RAY DIFFRACTION	99.08
3.11-3.42	0.2753	139	0.2331	1504	X-RAY DIFFRACTION	99.7
3.43-3.92	0.2296	134	0.1725	1520	X-RAY DIFFRACTION	99.58
3.92-4.94	0.2103	152	0.1445	1498	X-RAY DIFFRACTION	99.46
4.94-35.39	0.1817	166	0.1591	1595	X-RAY DIFFRACTION	99.1

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	2.11831492047	-0.327650265678	1.28507069493	4.56348722292	-0.982879104295	5.5055091711	-0.180591048307	-0.103636422933	0.311761229351	-0.305508243759	-0.0314580192181	-0.477604394739	-0.25968166413	0.130813228098	0.196696245501	0.263265391206	-0.0205826474879	0.0190015489194	0.249428763056	0.0194486565859	0.431371339352	31.4043024792	22.6941709051	-27.7537290499
2	1.86165054403	2.63029321214	-0.183025567502	3.74461653228	-0.503595334235	5.41491193328	0.132522847606	-0.144126542047	0.96446480423	-0.466061338865	-0.320238109992	0.0536923731856	-0.828476570814	-0.214910037431	0.104895621081	0.361967236554	-0.0083603056268	0.0238139572335	0.304548229256	0.0110793202742	0.500751245732	33.4484499088	29.0353800135	-32.3047739192
3	9.82595115846	2.14156063355	0.0366817984966	5.2660787224	-0.38492572777	5.27821719627	-0.102929489391	1.01343015561	-0.475104470699	-0.833909052253	0.300427242249	0.387066102102	0.381605155737	-0.161957377257	-0.180216522902	0.548687196069	-0.0264241686375	-0.0745375336304	0.428922506934	-0.0290746486182	0.303955174668	24.0099147095	21.3010601006	-40.9722627579
4	3.79784960548	-1.32054899889	0.648609470559	6.83193301908	-1.35974261175	4.06858705233	0.286910226912	0.238326507057	-0.665139911912	-0.704448425123	-0.151634250951	-0.368667059014	0.463548135342	0.589601303342	-0.00351510921722	0.425401186109	0.0695989420766	0.0443986683859	0.371919072954	-0.0414669363436	0.447702068311	30.5280762514	13.6950105878	-33.7216413758
5	1.70185136498	-0.5308403772	0.731191160006	5.64212946507	-1.97589143708	1.73196846307	0.188207906547	-0.118143124621	-0.529009819677	0.0144359088613	-0.054700361717	-0.0828273749096	0.14179273154	-0.281978211864	-0.230659375277	0.241587520537	-0.0446955281903	-0.0951964324664	0.398278678132	-0.0177504592816	0.433419109679	23.516514606	13.9702117398	-24.6058379575
6	2.25215469168	0.562453368524	3.98160164401	9.37415493647	0.369749367917	7.10251252902	-0.22823725291	-0.774192085488	-0.319660617008	-0.0364880980546	0.453473535156	1.80048220988	0.267762532109	-1.21345120221	-0.0867950248345	0.415040895706	0.00907152564819	0.0117216352107	0.606183896319	0.0595265105188	0.595942624207	13.8564088187	25.5324210062	-15.8674623937
7	7.06293393714	-4.53696233471	-0.587063089484	4.54433664389	0.400386405099	2.0940481838	0.0439216699274	0.361150606322	-1.12965708047	0.456445085795	-0.304408163963	0.600557547624	-0.0422129351911	0.36183562782	0.233597794456	0.406493024285	-0.0671082130332	-0.0518149654974	0.384310750785	0.0254916299173	0.491814543355	22.6907021891	7.85726058277	-18.8820212959
8	2.19744655313	3.42610576585	1.47986340372	6.01690316428	4.06001609886	4.80726330432	0.389394403316	-0.185585704063	-0.558382996173	1.49793025497	-0.299941833443	-0.654301205012	0.539601012739	0.0676399486892	-0.0222536197036	0.516597376585	-0.0468581309663	-0.105417318434	0.365763340653	0.0527180777494	0.453622383306	31.0954317757	17.0594599431	-11.7906191905
9	2.511009066	-2.16149367084	0.266334444294	6.43587111404	-0.00325809291135	2.93172077288	-0.250097358879	-0.181220502856	0.19617742796	0.965154996926	0.0892622009344	-0.74243635518	-0.0696380359787	0.141256232845	0.115493142109	0.442157281969	0.00682907920348	-0.137817386302	0.322874029661	0.0325287992473	0.583606083467	-1.1993139056	14.6368869316	-17.0404478068
10	5.16759274314	-1.99443547789	1.52602910542	8.46882064941	-4.77911183456	2.72523158025	-0.187677190942	-0.969703502684	0.520352315586	2.46262714291	0.27067908319	0.493422666134	0.0405328839269	-0.0209450844373	-0.189277391118	1.47434559646	0.147034657388	0.16230672912	0.498997741596	0.00714913285709	0.434269694949	-5.47316501512	10.799900011	-2.12577085273
11	2.86275490131	-1.28406275883	-1.20617654689	9.28294209769	0.824343115964	2.21179051294	-0.0960827714303	0.0478914349942	0.136834470601	0.925534712846	-0.0325261511274	-0.0611847052367	-0.0797775920259	-0.175246989712	0.136612780243	0.456216384178	0.0335331669332	-0.0455668807942	0.34731626309	-0.00971915201023	0.505756606805	-7.80606055271	21.1578235208	-16.9898979164
12	2.56011443908	-1.53509206059	-0.705799532866	6.28187407551	3.64646043569	4.38995133433	0.18266569133	0.431845026749	0.171347460866	-1.22267503537	-0.275649741708	-0.940223615532	-0.172566959571	-0.0489163010067	0.0332856648536	0.531393367726	0.0737860715312	0.125067708299	0.404837361486	0.0384347925871	0.616365388295	-0.146963159204	19.260499112	-31.1806725539
13	6.62006995989	-0.96963310267	0.316899561611	7.15661908609	0.0970742525014	4.8767757988	-0.0737290164278	0.425023958954	-1.12046244367	-0.983758415908	-0.128368512172	-0.640485013066	0.740487661247	0.665237399909	0.170460618099	0.546269083767	0.0205372129591	0.0508006601024	0.375313281394	-0.0173911620375	0.653429389614	30.2994936438	9.80006914444	-27.160053468
14	8.11239156439	0.00202355323868	3.01983919933	5.02772188097	0.148235195587	6.08237494368	0.186054765021	0.271060953534	0.869554748194	0.506504808585	-0.436565327278	0.254364496812	-0.399310547041	-0.104883555242	0.224525685347	0.323520845318	0.0183307439648	0.0703024846119	0.30124518945	0.017531146004	0.361842796595	22.5759408169	26.9369939653	-17.5462318257

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 'A' and (resid 24 through 48 )	A	A	24 - 48	31 - 55
2	2	chain 'A' and (resid 49 through 59 )	A	A	49 - 59	56 - 66
3	3	chain 'A' and (resid 60 through 85 )	A	A	60 - 85	67 - 92
4	4	chain 'A' and (resid 86 through 96 )	A	A	86 - 96	93 - 103
5	5	chain 'A' and (resid 97 through 116 )	A	A	97 - 116	104 - 123
6	6	chain 'A' and (resid 117 through 126 )	A	A	117 - 126	124 - 133
7	7	chain 'A' and (resid 127 through 139 )	A	A	127 - 139	134 - 146
8	8	chain 'A' and (resid 140 through 158 )	A	A	140 - 158	147 - 165
9	9	chain 'B' and (resid -6 through 59 )	B	E	-6 - 59	1 - 66
10	10	chain 'B' and (resid 60 through 75 )	B	E	60 - 75	67 - 82
11	11	chain 'B' and (resid 76 through 139 )	B	E	76 - 139	83 - 146
12	12	chain 'B' and (resid 140 through 158 )	B	E	140 - 158	147 - 165
13	13	chain 'A' and (resid -6 through 8 )	A	A	-6 - 8	1 - 15
14	14	chain 'A' and (resid 9 through 23 )	A	A	9 - 23	16 - 30

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About Yorodumi

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Yorodumi