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- PDB-5scm: Crystal Structure of Dihydrofolate Reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 5scm
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-22
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / Mycobacterium tuberculosis / DHFR / NADP / Folate / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex / 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 conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
Chem-GHU / IODIDE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700059C United States
CitationJournal: to be published
Title: Crystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-22
Authors: Mayclin, S.J. / Fairman, J.W. / Dranow, D.M. / Conrady, D.G. / Fox III, D. / Lukacs, C.M. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E. / Abendroth, J.
History
DepositionDec 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Other / Structure summary
Category: pdbx_SG_project / pdbx_database_status / struct_keywords
Item: _pdbx_database_status.SG_entry / _struct_keywords.text
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)21,5969
Polymers19,8321
Non-polymers1,7648
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.920, 68.550, 77.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is a monomer, the same as asu

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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 H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: folA, dfrA, Rv2763c, MTV002.28c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WNX1, dihydrofolate reductase

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Non-polymers , 5 types, 154 molecules

#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GHU / ethyl 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoate


Mass: 388.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H28N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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 Å3/Da / Density % sol: 38.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MCSG1 condition H2: 0.2 M potassium iodide, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: FR-E+ Superbright / Wavelength: 1.5418 Å
DetectorType: Saturn 944+ / Detector: CCD / Date: Apr 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 19706 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.69 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.069 / Net I/σ(I): 23.62 / Num. measured all: 239767
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.65-1.690.870.3263.834273144013270.38692.2
1.69-1.740.9160.3214.527504140813770.35497.8
1.74-1.790.9650.2986.1410809135613410.31998.9
1.79-1.840.9760.2278.0511300134313360.24199.5
1.84-1.910.9830.1929.5811279128412840.204100
1.91-1.970.9920.15312.2311614125612540.16299.8
1.97-2.050.9910.13714.2511542119511950.145100
2.05-2.130.9950.11717.6512261120112000.12399.9
2.13-2.220.9960.1122.0713861110411040.114100
2.22-2.330.9970.10124.8114744107610760.105100
2.33-2.460.9970.09327.1714742102610240.09799.8
2.46-2.610.9980.08829.79147059559550.091100
2.61-2.790.9980.0833.42159989329310.08299.9
2.79-3.010.9990.06941.56175768628600.07199.8
3.01-3.30.9990.06148.59164427987970.06399.9
3.3-3.690.9990.05355.93146797257250.054100
3.69-4.260.9990.04762.68130196546540.048100
4.26-5.220.9990.04562.28107495505500.046100
5.22-7.380.9990.0556.0983334484480.052100
7.380.9990.0557.5643372702680.05199.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_1932refinement
PDB_EXTRACT3.11data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→38.725 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 986 5 %
Rwork0.1778 18717 -
obs0.1792 19703 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 185.12 Å2 / Biso mean: 18.397 Å2 / Biso min: 7.11 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 88 146 1488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061384
X-RAY DIFFRACTIONf_angle_d1.261895
X-RAY DIFFRACTIONf_chiral_restr0.056201
X-RAY DIFFRACTIONf_plane_restr0.005238
X-RAY DIFFRACTIONf_dihedral_angle_d20.454496
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6501-1.73710.29651320.24792508264095
1.7371-1.84590.21431390.19992622276199
1.8459-1.98850.20881390.174626562795100
1.9885-2.18850.2071400.168326662806100
2.1885-2.50520.19191430.170726992842100
2.5052-3.15610.2061420.182227042846100
3.1561-38.73560.19551510.166228623013100
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)
10.41220.1175-0.03051.61960.09480.68090.02360.19370.217-0.2106-0.00890.0282-0.25360.0029-0.01610.14730.00790.00610.14610.05370.123240.911410.82498.0961
22.6714-1.03710.90071.5325-0.48083.2483-0.0118-0.1687-0.01440.10440.0770.1435-0.013-0.234-0.04770.0846-0.00930.00590.0920.00460.085734.1561.499119.3491
32.3885-0.4837-0.25312.63630.9392.7244-0.01270.1504-0.0646-0.11240.04270.05960.1119-0.0714-0.00350.083-0.0078-0.02010.1040.00570.05636.5378-2.41543.3031
41.6175-0.3839-0.86931.04820.33692.40110.0865-0.10320.09930.15850.0358-0.1214-0.14620.1333-0.11570.1308-0.0235-0.02080.102-0.01670.117142.70697.593919.4223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 9 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 35 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 96 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 97 through 159 )A0

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