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- PDB-5u26: Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Red... -

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Basic information

Entry
Database: PDB / ID: 5u26
TitleCrystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound to NADP and p218 Inhibitor
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / Folate / 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
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound to NADP and p218 Inhibitor
Authors: Mayclin, S.J. / Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Oct 4, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1906
Polymers19,8321
Non-polymers1,3585
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-18 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.050, 66.980, 77.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate reductase


Mass: 19832.365 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: folA, folA_1, BN1213_03327, BN1303_00864, ERS007661_02580, ERS007663_03946, ERS007665_02766, ERS007741_00337, ERS013471_00736, ERS023446_01268, ERS024213_02711, ERS027644_04978, ERS027646_ ...Gene: folA, folA_1, BN1213_03327, BN1303_00864, ERS007661_02580, ERS007663_03946, ERS007665_02766, ERS007741_00337, ERS013471_00736, ERS023446_01268, ERS024213_02711, ERS027644_04978, ERS027646_03318, ERS027653_04780, ERS027654_00299, ERS027656_00246, ERS027659_04151, ERS027661_03595, ERS027666_04095, ERS031537_04020, ERS124361_01473, RN05_2938
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0E8UVJ4, UniProt: P9WNX1*PLUS, dihydrofolate reductase

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Non-polymers , 5 types, 129 molecules

#2: 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.: 1 / Source method: obtained synthetically / Formula: C18H24N4O4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 1.93 Å3/Da / Density % sol: 32 % / Mosaicity: 0.18 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Mycobacterium tuberculosis DHFR, R9978 at 10 mg/ml, Batch number BOS051006 against RigakuReagents Ammonium Sulfate Screen, condition B10: 2.2M ammonium sulfate + 0.2M potassium acetate; 20% ...Details: Mycobacterium tuberculosis DHFR, R9978 at 10 mg/ml, Batch number BOS051006 against RigakuReagents Ammonium Sulfate Screen, condition B10: 2.2M ammonium sulfate + 0.2M potassium acetate; 20% EG cryo; crystal tracking ID 255057b10 (puck gel2-3)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 12959 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 15.4 % / Biso Wilson estimate: 14.39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Net I/σ(I): 23.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2% possible all
1.85-1.90.5824.3288170.90186.8
1.9-1.950.4735.260.94687.8
1.95-2.010.4125.990.94693.2
2.01-2.070.3377.420.96292.8
2.07-2.140.2779.340.97699.1
2.14-2.210.23111.970.98596
2.21-2.290.2312.440.98697.3
2.29-2.390.19714.980.9998.4
2.39-2.490.17716.220.99296.9
2.49-2.620.14420.070.99598.9
2.62-2.760.15219.290.99497.8
2.76-2.930.11626.610.99897.6
2.93-3.130.09433.840.998100
3.13-3.380.07142.10.99998.8
3.38-3.70.05952.870.99999.1
3.7-4.140.04763.281100
4.14-4.780.0469.7199.8
4.78-5.850.04956.39199.7
5.85-8.270.05153.070.999100
8.270.04166.73198.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_1702refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DFR

7dfr


Resolution: 1.85→33.463 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.51
RfactorNum. reflection% reflection
Rfree0.1915 645 4.98 %
Rwork0.1479 --
obs0.1501 12959 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.16 Å2 / Biso mean: 17.0744 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: final / Resolution: 1.85→33.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1277 0 88 124 1489
Biso mean--20.05 27.22 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181431
X-RAY DIFFRACTIONf_angle_d1.7241968
X-RAY DIFFRACTIONf_chiral_restr0.089209
X-RAY DIFFRACTIONf_plane_restr0.015246
X-RAY DIFFRACTIONf_dihedral_angle_d18.187523
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.99280.20161090.16252231234089
1.9928-2.19340.20981250.1492409253496
2.1934-2.51060.22751200.15232473259397
2.5106-3.16280.19971380.15742531266999
3.1628-33.46890.16691530.136726702823100
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)
10.7484-0.2544-0.46712.99913.47965.3358-0.09440.1623-0.07090.0037-0.13840.15380.18270.00740.17340.04860.01470.01770.1044-0.02190.0993-10.5579-12.09945.8915
21.3884-1.17470.11752.1975-0.06911.0786-0.0397-0.00260.06680.18760.1173-0.1672-0.29140.1573-0.10280.1304-0.02040.01130.0761-0.03340.0843-8.33273.051421.3626
32.0989-0.66051.36121.8842-0.9112.12150.09840.04810.0533-0.1235-0.0794-0.1169-0.18180.26520.0020.0254-0.01370.0230.10920.00680.0769-3.485-1.43128.9364
43.4866-2.0713-1.45783.01570.90854.87940.0375-0.01630.60410.1359-0.1006-0.5854-0.2930.3389-0.04330.0618-0.0201-0.0050.17250.05330.1510.68994.19645.8827
53.9562-1.55820.88364.6393-0.23223.96440.02920.1230.4112-0.09340.0152-0.0898-0.37380.1297-0.02630.1101-0.00090.01080.10510.03450.1014-9.86817.4647-1.2702
62.1495-1.78940.11727.6592-1.45831.06880.01060.3407-0.1081-0.69680.03530.33360.24980.0433-0.01720.1560.0059-0.02070.16270.01610.1151-13.4096-2.4946-3.6241
71.29691.2761-0.35233.1350.69732.01950.11390.2210.0744-0.1587-0.06620.2088-0.0093-0.03360.00270.07910.03040.00040.0839-0.00260.0626-14.7264-5.00977.1392
82.32422.06452.63862.62832.59243.11410.1753-0.0186-0.14320.1428-0.0109-0.04690.1577-0.0548-0.06920.06610.0127-0.01740.0737-0.02650.0849-9.6229-10.32615.7527
96.4176-6.02174.06245.6542-3.79712.6013-0.3315-0.551-0.09860.47120.48660.4503-0.3374-0.233-0.05220.22890.05480.03460.1571-0.02580.1823-13.79583.422426.5486
101.68770.75360.23061.0740.14881.53260.104-0.1666-0.08760.41640.03830.59990.2119-0.1461-0.08910.0982-0.00970.00890.12010.03360.1822-17.2958-12.631616.9923
115.85020.10750.87924.21652.03675.48660.1905-0.19840.080.1217-0.1292-0.1920.20980.04830.00120.0533-0.0075-0.01370.11410.01080.07240.5757-8.002628.2581
124.370.19894.07980.53660.795.34140.3703-0.1245-0.23960.1778-0.18930.17360.4838-0.2039-0.20740.1365-0.0206-0.00550.08320.00280.1029-10.4621-14.787217.012
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 9 )A-6 - 9
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 24 )A10 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 49 )A25 - 49
4X-RAY DIFFRACTION4chain 'A' and (resid 50 through 60 )A50 - 60
5X-RAY DIFFRACTION5chain 'A' and (resid 61 through 76 )A61 - 76
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 89 )A77 - 89
7X-RAY DIFFRACTION7chain 'A' and (resid 90 through 106 )A90 - 106
8X-RAY DIFFRACTION8chain 'A' and (resid 107 through 115 )A107 - 115
9X-RAY DIFFRACTION9chain 'A' and (resid 116 through 125 )A116 - 125
10X-RAY DIFFRACTION10chain 'A' and (resid 126 through 139 )A126 - 139
11X-RAY DIFFRACTION11chain 'A' and (resid 140 through 150 )A140 - 150
12X-RAY DIFFRACTION12chain 'A' and (resid 151 through 159 )A151 - 159

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