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- PDB-6dav: Crystal Structure of Human DHFR complexed with NADP and N10formyl... -

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Basic information

Entry
Database: PDB / ID: 6dav
TitleCrystal Structure of Human DHFR complexed with NADP and N10formyltetrahydrofolate
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Structure-guided Drug Discovery Consortium / dihydrofolate reductase / hDHFR / NADP
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-G3V / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsMayclin, S.J. / Dranow, D.M. / Lorimer, D.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
CitationJournal: to be published
Title: Crystal Structure of Human DHFR complexed with NADP and N10formyltetrahydrofolate
Authors: Mayclin, S.J. / Dranow, D.M. / Walpole, C. / Lorimer, D.D.
History
DepositionMay 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5759
Polymers42,9612
Non-polymers2,6147
Water5,909328
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7574
Polymers21,4811
Non-polymers1,2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8195
Polymers21,4811
Non-polymers1,3384
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.090, 42.740, 72.290
Angle α, β, γ (deg.)91.050, 101.880, 120.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Dihydrofolate reductase /


Mass: 21480.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-G3V / N-(4-{[(2,4-diaminopteridin-6-yl)methyl](hydroxymethyl)amino}benzene-1-carbonyl)-L-glutamic acid


Mass: 470.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O6
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 328 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Wizard 3/4 H10 (296175h10): 100 mM Tris base/ Hydrochloric acid pH 8.5, 30% (w/v) PEG3350, 30% (v/v) 2-propanol, protein conc. 28.74 mg/mL, protein batch ID XP819, 10 mM NADP, 3.75 mM ...Details: Wizard 3/4 H10 (296175h10): 100 mM Tris base/ Hydrochloric acid pH 8.5, 30% (w/v) PEG3350, 30% (v/v) 2-propanol, protein conc. 28.74 mg/mL, protein batch ID XP819, 10 mM NADP, 3.75 mM BSI108214, seeded from 293949g10, cryoprotected with 20% eg, puck izs6-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 12, 2018
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 50838 / % possible obs: 94 % / Redundancy: 2.309 % / Biso Wilson estimate: 21.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.04 / Χ2: 1.068 / Net I/σ(I): 13.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.592.3390.3952.1137480.8950.50894.5
1.59-1.632.2320.3532.3936820.9160.45594
1.63-1.682.3550.2723.0736300.9460.3594.7
1.68-1.732.2770.2223.7934610.9610.28695
1.73-1.792.4130.1635.0534070.9780.20995
1.79-1.852.3780.1296.4432890.9830.16694.6
1.85-1.922.270.104831380.9880.13494.7
1.92-22.350.07310.6630200.9950.09494.6
2-2.092.2520.06212.5328920.9950.08193.7
2.09-2.192.3690.05315.327640.9960.06993.8
2.19-2.312.3350.04417.6826100.9970.05793.2
2.31-2.452.210.04119.5224070.9970.05392
2.45-2.622.3280.03323.1622760.9980.04291.7
2.62-2.832.2220.03124.6621520.9980.0492.3
2.83-3.12.3420.02728.9219630.9980.03491.2
3.1-3.472.1850.02630.2117380.9980.03392.1
3.47-42.2990.02333.5216180.9980.02994.9
4-4.92.3270.01934.5813710.9990.02495.7
4.9-6.932.250.0233.610770.9990.02597
6.93-502.3610.01935.35950.9990.02498

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
Cootmodel building
RefinementResolution: 1.55→36.64 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.2
RfactorNum. reflection% reflection
Rfree0.2044 2028 3.99 %
Rwork0.1652 --
obs0.1668 50797 93.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.18 Å2 / Biso mean: 32.178 Å2 / Biso min: 16.19 Å2
Refinement stepCycle: final / Resolution: 1.55→36.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2982 0 176 331 3489
Biso mean--26.81 40.36 -
Num. residues----372
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5499-1.58860.27691460.26473462360894
1.5886-1.63160.26781500.25533499364994
1.6316-1.67960.32511260.22983550367694
1.6796-1.73380.30761330.21953480361395
1.7338-1.79580.25661520.20653513366595
1.7958-1.86770.24251390.1873545368495
1.8677-1.95270.22011370.18673538367595
1.9527-2.05560.2231360.17853483361994
2.0556-2.18440.25191330.18363480361394
2.1844-2.3530.23361480.17773440358893
2.353-2.58970.2111630.17363384354792
2.5897-2.96430.2031490.1653402355192
2.9643-3.73420.16771510.14213433358492
3.7342-36.64260.17551650.13593560372597
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
16.0313-1.77081.63424.3523-0.13252.8644-0.11740.00720.01590.08160.13560.12130.05770.23480.00710.1258-0.02170.01590.15860.00150.1438-1.021611.184122.9352
26.2076-1.30743.09295.8998-6.31047.47930.10760.1857-0.5417-0.41560.06550.11850.79540.0508-0.21560.293-0.01350.00460.1714-0.04470.2681-3.03912.344114.4184
34.69410.43351.45983.483-0.01243.9282-0.06110.2019-0.1422-0.26590.0638-0.02520.20670.0747-0.01070.1744-0.02230.02740.15950.00190.12042.201512.19737.9925
48.77521.1864-1.6791.0318-1.48862.1487-0.04690.19440.432-0.26490.1328-0.2795-0.26270.6558-0.14160.3129-0.0580.00180.29220.07110.25219.995222.78297.0979
52.91512.56711.69084.1950.82542.3802-0.23140.29660.2338-0.46810.17660.3865-0.0391-0.03270.06720.3228-0.0365-0.02270.24860.06160.2676-4.495522.09982.0169
63.2991.17022.71018.97634.45599.3996-0.1781-0.01950.5632-0.2910.0370.762-0.35340.00160.05430.1426-0.03030.0120.1617-0.00210.2755-5.067520.099517.1198
75.9662-4.10422.6495.809-1.78037.0423-0.0050.23790.5091-0.1972-0.1440.1161-0.23530.05420.19990.1546-0.0437-0.01470.17250.03530.2942-11.396214.356819.0543
83.75411.9571-1.76793.4595-3.8914.60010.106-0.444-0.08610.4776-0.0868-0.1224-0.06980.2091-0.0060.23050.03030.00970.303-0.02920.19460.743811.896430.9502
93.96983.56343.47739.13640.68058.9239-0.2378-0.68420.42380.3012-0.02430.4663-0.0625-0.75950.20740.17920.05010.03380.2826-0.00570.2707-16.574818.404125.676
106.6889-3.20452.7713.9227-1.33623.2243-0.0364-0.237-0.3252-0.16980.20750.41410.2096-0.2728-0.21140.2153-0.0480.01010.18040.03780.2442-12.18794.572922.0911
115.7476-0.56861.94382.59340.14324.4054-0.0392-0.0876-0.0217-0.02060.16910.09550.10680.2026-0.11560.14220.02750.02530.1377-0.00570.1205-14.537429.77744.3435
121.6966-0.13130.26011.9553-1.41982.99430.0206-0.1484-0.207-0.01160.13050.00460.75170.2911-0.13260.31520.0644-0.04340.1894-0.00720.2089-14.046917.577848.6084
134.00220.13020.67233.6543-0.52076.66410.0866-0.262-0.2573-0.00640.10710.38330.2852-0.4057-0.17150.2347-0.03140.01570.16960.06520.2069-20.532519.473559.0212
142.7323-2.22711.55253.09650.3993.16820.3514-0.0002-0.2476-0.3216-0.14820.24360.95340.3915-0.04140.31530.04430.00270.2795-0.01430.2188-9.071114.648859.4735
152.7303-1.5018-0.63332.22920.18284.16670.019-0.24150.13650.12250.0659-0.19920.05440.6693-0.05680.1689-0.02110.01410.2361-0.00010.1952-5.924629.689844.9781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 28 )A2 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 40 )A29 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 76 )A41 - 76
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 88 )A77 - 88
5X-RAY DIFFRACTION5chain 'A' and (resid 89 through 112 )A89 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 127 )A113 - 127
7X-RAY DIFFRACTION7chain 'A' and (resid 128 through 139 )A128 - 139
8X-RAY DIFFRACTION8chain 'A' and (resid 140 through 149 )A140 - 149
9X-RAY DIFFRACTION9chain 'A' and (resid 150 through 159 )A150 - 159
10X-RAY DIFFRACTION10chain 'A' and (resid 160 through 187 )A160 - 187
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 28 )B2 - 28
12X-RAY DIFFRACTION12chain 'B' and (resid 29 through 60 )B29 - 60
13X-RAY DIFFRACTION13chain 'B' and (resid 61 through 101 )B61 - 101
14X-RAY DIFFRACTION14chain 'B' and (resid 102 through 118 )B102 - 118
15X-RAY DIFFRACTION15chain 'B' and (resid 119 through 187 )B119 - 187

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