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

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Basic information

Entry
Database: PDB / ID: 5scr
TitleCrystal Structure of Dihydrofolate Reductase from Mycobacterium tuberculosis bound to NADP and SDDC Inhibitor SDDC-735
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
Chem-GXJ / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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-735
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)20,9503
Polymers19,8321
Non-polymers1,1182
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.910, 67.480, 78.650
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

#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
#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-GXJ / (2R)-3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)-2-methylpropanoic acid


Mass: 374.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H26N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
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 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: Wizard 3/4 B6: 20% PEG 6000, 100mM Citric acid/ NaOH pH4.0, 100mM LiCl; r9978 at 39.8mg/mL w/ 3.75mM EBSI5524 amd 10mM NADP, tray 266660b6; puck kqt0-14; cryo 25% eg

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: Rotating Copper Anode / Type: FRE+ Superbright / Wavelength: 1.5418 Å
DetectorType: Saturn 944+ / Detector: CCD / Date: Oct 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 12061 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.87 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.104 / Χ2: 0.893 / Net I/σ(I): 17.77 / Num. measured all: 123939
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-20.3734.241849048030.8730.41588.8
2-2.060.3085.5949458468250.9130.33897.5
2.06-2.120.2957.3166838498460.9430.31699.6
2.12-2.180.2510.2686707977970.9710.262100
2.18-2.250.2411191478058050.980.253100
2.25-2.330.23411.3286067567560.9840.245100
2.33-2.420.19912.8583927287280.9910.208100
2.42-2.520.19912.3783297227220.9890.208100
2.52-2.630.17513.7878906816810.9930.183100
2.63-2.760.14915.5577106646640.9930.156100
2.76-2.910.12716.8873766336330.9950.133100
2.91-3.080.120.4669265935930.9970.105100
3.08-3.30.08224.4765735665660.9980.086100
3.3-3.560.07130.8259385225220.9980.075100
3.56-3.90.05939.152654884880.9990.062100
3.9-4.360.05142.8647484514430.9990.05398.2
4.36-5.030.0542.0142894064030.9990.05299.3
5.03-6.170.05833.9238433443440.9990.061100
6.17-8.720.04935.0228932742740.9990.052100
8.720.0444.8115321701680.9990.04298.8

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.11data extraction
PHENIXmodel building
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→33.977 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 603 5 %
Rwork0.1684 11458 -
obs0.1708 12061 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.4 Å2 / Biso mean: 19.7511 Å2 / Biso min: 0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 75 128 1485
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061423
X-RAY DIFFRACTIONf_angle_d0.9471951
X-RAY DIFFRACTIONf_chiral_restr0.056204
X-RAY DIFFRACTIONf_plane_restr0.004248
X-RAY DIFFRACTIONf_dihedral_angle_d18.973801
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.14620.25911420.18842725286796
2.1462-2.45660.25111500.180428432993100
2.4566-3.09480.24321520.186628723024100
3.0948-33.98160.17941590.148930183177100
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)
11.64410.032-0.15422.78131.33942.68420.0866-0.0622-0.04-0.0206-0.0647-0.1167-0.04110.0026-0.05740.0511-0.0005-0.01110.1222-0.00410.1068-9.5456-4.3314.5807
22.6595-0.78550.52432.2399-0.48321.87960.047-0.02770.00130.01690.0072-0.1104-0.09320.2039-0.05560.0553-0.00050.00560.181-0.0140.1113-1.7383-0.40959.595
31.36790.11780.75580.9191-0.20612.09250.0682-0.04970.02980.0522-0.02220.0488-0.0101-0.0408-0.060.07810.00480.01480.1133-0.02370.1006-11.8281-4.524312.8674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -6 through 24 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 60 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 159 )A0

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