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- PDB-5sd0: Crystal Structure of Dihydrofolate Reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 5sd0
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-1225
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 / glycine biosynthetic 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 domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / Chem-HIK / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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-1225
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)21,2539
Polymers19,8321
Non-polymers1,4218
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.480, 67.130, 72.140
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 / Fragment: MtDHFR
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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WNX1, dihydrofolate reductase

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Non-polymers , 6 types, 192 molecules

#2: 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
#3: Chemical ChemComp-HIK / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}pyridin-3-yl)propan-1-ol


Mass: 347.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H25N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 1.8 Å3/Da / Density % sol: 32 % / Mosaicity: 0.173 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: MCSG4 F7 (291338f7): 200mM magnesium formate, 100mM MES:NaOH pH6.5, 25% (w/v) PEG4000, 10mg/mL protein conc., cryo 15% ethylene glycol, puck pwp0-15

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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: PAD / Date: May 17, 2017
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 15006 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.867 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.078 / Net I/σ(I): 15.95 / Num. measured all: 87095
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
1.75-1.80.7970.52.353190108610430.696
1.8-1.840.9060.3743.614110106910580.43499
1.84-1.90.9350.3334.925105103110300.37399.9
1.9-1.960.9750.2517.095888100310030.276100
1.96-2.020.9830.2078.8963569749730.22599.9
2.02-2.090.9870.1899.8862039579570.206100
2.09-2.170.9920.14311.9157119169160.156100
2.17-2.260.9940.12613.0955978778760.13799.9
2.26-2.360.9950.11414.7656008518510.124100
2.36-2.470.9960.09816.6153458188170.10699.9
2.47-2.610.9950.08419.3848117747730.09299.9
2.61-2.770.9960.07721.0247097407400.083100
2.77-2.960.9970.06624.2545046986980.071100
2.96-3.20.9980.05827.2941786536530.063100
3.2-3.50.9980.04930.737385995990.054100
3.5-3.910.9990.04234.234235535530.046100
3.91-4.520.9990.03836.7730854914910.042100
4.52-5.530.9990.03935.2225094314300.04299.8
5.53-7.830.9980.04233.2419943373370.045100
7.830.9980.03534.9510392092080.0499.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXdev_2744refinement
PDB_EXTRACT3.22data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→49.144 Å / Occupancy max: 1 / Occupancy min: 0.29 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1858 1600 10.66 %
Rwork0.1453 13404 -
obs0.1497 15004 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.44 Å2 / Biso mean: 21.4083 Å2 / Biso min: 9.76 Å2
Refinement stepCycle: LAST / Resolution: 1.75→49.144 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1294 0 93 184 1571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061459
X-RAY DIFFRACTIONf_angle_d0.8911983
X-RAY DIFFRACTIONf_chiral_restr0.054203
X-RAY DIFFRACTIONf_plane_restr0.006268
X-RAY DIFFRACTIONf_dihedral_angle_d20.957855
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7499-1.80640.26721240.22471149127396
1.8064-1.8710.28771450.207611981343100
1.871-1.94590.25211360.172712221358100
1.9459-2.03440.21611420.148511771319100
2.0344-2.14170.20961450.151912201365100
2.1417-2.27590.191410.152712121353100
2.2759-2.45160.181630.156212081371100
2.4516-2.69830.18441280.14912341362100
2.6983-3.08870.19481440.142212291373100
3.0887-3.89120.15261560.124312421398100
3.8912-49.16320.15971760.125813131489100
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)
10.56160.08190.00374.398-4.564.39070.05650.12540.0745-0.245-0.00910.03890.05360.2016-0.0410.11470.0054-0.01070.12710.00710.107914.392612.93086.5272
22.6420.88830.18212.27661.34381.25090.1439-0.171-0.25780.1988-0.0115-0.1670.1767-0.0577-0.14260.2016-0.0137-0.03110.13870.0380.133811.0387-0.324623.2961
33.87-1.7274-4.09444.79680.06425.06870.0760.0286-0.25850.0227-0.07870.23580.2701-0.4983-0.01110.1301-0.0185-0.01570.19-0.00360.17722.68868.24614.1932
43.3301-1.72030.10074.2391-0.19941.79130.04940.0559-0.117-0.079-0.0561-0.05690.0892-0.02810.00540.1222-0.0105-0.00720.1261-0.00640.103410.5731-3.86235.0249
50.67-2.27860.58049.4774-3.23031.6707-0.12660.08160.26-0.2234-0.0086-0.5553-0.14790.04040.1570.2365-0.00990.02430.1905-0.00490.228618.36052.7949-1.4777
63.48660.89240.37134.9213-1.33293.51240.07190.0901-0.0192-0.1768-0.042-0.21950.03460.0625-0.03390.11720.0084-0.00010.1117-0.01840.096118.57126.27398.8189
72.0083-0.2313-0.3580.63210.80231.89770.1112-0.1881-0.0260.13040.0273-0.07-00.1023-0.12660.1335-0.0191-0.02870.1303-0.00180.141117.74019.928620.6538
88.10567.2941-0.41828.90060.35660.6950.0463-0.12520.1123-0.09550.08270.23180.0748-0.2359-0.16550.1629-0.01880.00460.1662-0.00940.12142.506211.926928.1651
94.72891.6649-6.58553.1381-2.02649.2075-0.00590.04620.2749-0.23430.0349-0.15170.17810.1118-0.19710.166-0.0146-0.00210.16320.02280.180114.068916.614517.8851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 9 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 24 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 35 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 76 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 77 through 89 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 90 through 106 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 107 through 139 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 140 through 150 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 151 through 159 )A0

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