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

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Basic information

Entry
Database: PDB / ID: 5ujf
TitleCrystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound p218 Inhibitor
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / Folate / p218 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


NADP+ binding / dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / 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-MMV / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound p218 Inhibitor
Authors: Mayclin, S.J. / Fairman, J.W. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6746
Polymers19,9641
Non-polymers7115
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-36 kcal/mol
Surface area8080 Å2
2
A: Dihydrofolate reductase
hetero molecules

A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,34812
Polymers39,9272
Non-polymers1,42110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area2370 Å2
ΔGint-93 kcal/mol
Surface area15310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.490, 59.490, 102.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Dihydrofolate reductase


Mass: 19963.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / 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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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: 2.63 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystal Screen HT condition C6: 200mM Ammonium sulfate, 30% (w/v) PEG 8000, protein conc. 10 mg/ml, cryo 20% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9811 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.468 % / Biso Wilson estimate: 45.28 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.05 / Χ2: 0.977 / Net I/σ(I): 29.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.367.6130.5674.137100.9240.60899.9
2.36-2.427.6570.4624.957060.9620.496100
2.42-2.497.6550.386.056670.9670.408100
2.49-2.577.6440.297.646550.9720.312100
2.57-2.667.620.2279.396230.9850.244100
2.66-2.757.6110.18411.836280.990.197100
2.75-2.857.5820.14114.586050.9940.152100
2.85-2.977.6140.10718.515780.9960.114100
2.97-3.17.5630.07524.465330.9980.08100
3.1-3.257.5390.06130.45230.9980.065100
3.25-3.437.5230.04537.985110.9990.049100
3.43-3.647.4710.0443.124800.9990.043100
3.64-3.897.4460.03152.824480.9990.033100
3.89-4.27.390.02661.754280.9990.028100
4.2-4.67.2420.02468.2440010.026100
4.6-5.147.2130.02371.143560.9990.025100
5.14-5.947.2150.02267.533110.024100
5.94-7.276.8640.02368.7827210.025100
7.27-10.296.5960.01876.222510.019100
10.29-505.50.01869.5413210.0297.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(phenix.refine: dev_1615)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1df7

1df7


Resolution: 2.3→50 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 25.08
RfactorNum. reflection% reflection
Rfree0.2274 542 5.53 %
Rwork0.1786 --
obs0.1814 9803 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.34 Å2 / Biso mean: 57.14 Å2 / Biso min: 27.15 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 45 29 1272
Biso mean--55.12 48.26 -
Num. residues----161
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071271
X-RAY DIFFRACTIONf_angle_d0.9111737
X-RAY DIFFRACTIONf_chiral_restr0.036187
X-RAY DIFFRACTIONf_plane_restr0.005221
X-RAY DIFFRACTIONf_dihedral_angle_d12.426433
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3001-2.53150.26681060.22472288
2.5315-2.89780.23371620.20752252
2.8978-3.65070.24771320.19142308
3.6507-500.21091420.15832413
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)
12.7307-0.4647-0.13171.8610.72512.91690.2238-0.18020.1030.3955-0.0306-0.11260.1678-0.1473-0.20030.3619-0.0892-0.01930.2781-0.01820.330420.8634-23.0785-6.3324
21.46120.08050.54243.6394-2.64528.2980.07130.0703-0.46520.15010.1262-0.05791.8264-0.1633-0.17430.6243-0.0317-0.07750.334-0.04690.445125.5202-31.2864-3.7233
38.23440.7155-1.47412.3158-2.52844.6702-0.24040.6134-2.1448-0.40950.2913-0.49191.8779-0.4169-0.03771.161-0.1141-0.05090.5016-0.08340.801523.6018-38.7063-4.0722
47.37351.11720.22366.8751.34865.50330.5012-0.5817-1.14280.3884-0.51020.0561.5426-0.4621-0.18671.074-0.0972-0.12930.57440.19240.637621.2516-37.25288.3665
58.92350.1221-5.04317.16064.89176.35390.302-2.22940.3489-0.30830.73060.11-0.30891.784-0.25631.426-0.3234-0.29420.97690.26360.481426.8235-31.651512.3245
62.50211.19740.43832.89571.36126.93570.2049-0.3281-0.10280.57950.0247-0.00880.15330.609-0.2370.4323-0.0898-0.0120.3086-0.05560.34526.9175-21.97911.7711
76.8373.063-5.02453.0173-3.04694.12981.1870.88611.51420.8840.54861.9395-0.9891-1.7214-1.68290.54270.05330.11150.69880.08750.929210.5643-18.1606-10.2141
81.25071.18082.53015.25392.37925.3183-0.50150.54080.2442-0.33420.4776-0.2923-0.40390.70580.06030.5408-0.1730.03110.4087-0.02770.350226.7199-11.5583-0.9774
92.5586-0.2707-0.92291.7076-1.93384.8486-0.2275-0.10250.3693-0.3905-0.1893-0.1743-1.49770.20120.13790.3466-0.0640.05710.421-0.07860.372427.9496-17.2446-13.8294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 24 )A-1 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 49 )A25 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 60 )A50 - 60
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 76 )A61 - 76
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 87 )A77 - 87
6X-RAY DIFFRACTION6chain 'A' and (resid 88 through 115 )A88 - 115
7X-RAY DIFFRACTION7chain 'A' and (resid 116 through 125 )A116 - 125
8X-RAY DIFFRACTION8chain 'A' and (resid 126 through 139 )A126 - 139
9X-RAY DIFFRACTION9chain 'A' and (resid 140 through 159 )A140 - 159

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