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- PDB-5u27: Crystal Structure of Mycobacterium tuberculosis Dihydrofolate Red... -

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Basic information

Entry
Database: PDB / ID: 5u27
TitleCrystal Structure of Mycobacterium tuberculosis Dihydrofolate Reductase Bound to NADP and p65 Inhibitor
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Chem-P65 / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 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 p65 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1406
Polymers19,8321
Non-polymers1,3075
Water2,162120
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint10 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.730, 66.550, 77.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-P65 / 2,4-diamino-6-methyl-5-[3-(2,4,5-trichlorophenoxy)propyloxy]pyrimidine


Mass: 377.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15Cl3N4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 36.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Mycobacterium tuberculosis DHFR, R9978 at 14.76 mg/ml, Batch number 1639001 against Microlytic MCSG1 Screen, condition H6: 0.1 M Sodium Acetate:HCl pH 4.6, 3.5 M Sodium formate ; crystal ...Details: Mycobacterium tuberculosis DHFR, R9978 at 14.76 mg/ml, Batch number 1639001 against Microlytic MCSG1 Screen, condition H6: 0.1 M Sodium Acetate:HCl pH 4.6, 3.5 M Sodium formate ; crystal tracking ID 256965h6 (puck fpd7-3)

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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: Aug 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 10006 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.04 % / Biso Wilson estimate: 19.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.074 / Net I/σ(I): 15.34
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
2.05-2.10.2534.160.897184.7
2.1-2.160.1985.470.947191.1
2.16-2.220.1776.740.965197.9
2.22-2.290.1997.870.967199.3
2.29-2.370.1699.780.9831100
2.37-2.450.1610.340.9831100
2.45-2.540.14511.570.9871100
2.54-2.650.11913.080.9911100
2.65-2.760.11913.080.9891100
2.76-2.90.08915.940.9951100
2.9-3.060.08416.860.9941100
3.06-3.240.06821.160.9971100
3.24-3.470.05823.440.9971100
3.47-3.740.05326.760.9981100
3.74-4.10.04928.930.9971100
4.1-4.580.04530.280.998199.5
4.58-5.290.04529.150.997199.7
5.29-6.480.05125.20.9981100
6.48-9.170.04327.230.9981100
9.17-500.03629.710.998197.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(phenix.refine: dev_1769)refinement
PDB_EXTRACT3.2data extraction
PHASERphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DFR

7dfr


Resolution: 2.05→33.519 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.6
RfactorNum. reflection% reflection
Rfree0.211 515 5.15 %
Rwork0.1663 --
obs0.1686 10004 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 53.32 Å2 / Biso mean: 20.1508 Å2 / Biso min: 8.83 Å2
Refinement stepCycle: final / Resolution: 2.05→33.519 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 83 120 1476
Biso mean--17.37 30.37 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051428
X-RAY DIFFRACTIONf_angle_d1.1491961
X-RAY DIFFRACTIONf_chiral_restr0.045208
X-RAY DIFFRACTIONf_plane_restr0.004247
X-RAY DIFFRACTIONf_dihedral_angle_d19.301524
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 (%)
2.05-2.25630.24071090.17552187229692
2.2563-2.58260.23521380.177523702508100
2.5826-3.25340.20271370.180523972534100
3.2534-33.52370.1971310.151225352666100
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)
11.3547-0.5529-1.40725.03124.49696.09080.07090.2191-0.1546-0.3096-0.1563-0.0282-0.098-0.12050.1040.12430.0509-0.02930.1464-0.04480.1856-10.5936-11.80586.0638
20.6617-0.2782-0.01431.0286-0.95591.77710.12410.06790.00240.1368-0.1264-0.1646-0.01380.33010.00350.11230.0007-0.04620.1577-0.02760.145-5.43030.163113.3768
31.07290.3753-0.82610.3873-0.68512.81020.07140.28370.0162-0.1798-0.2301-0.2255-0.16160.48860.04940.0973-0.00110.00120.3349-0.01480.19760.89763.70196.2938
45.8701-2.73550.3044.3807-0.55543.10350.14210.10990.1907-0.0888-0.0179-0.0167-0.23290.407-0.08670.1074-0.0030.03570.1558-0.01520.1268-9.697.19-0.997
51.22840.9481-0.10612.3686-0.82361.30990.05690.2091-0.0617-0.20070.06120.08190.27560.1293-0.1050.11740.0354-0.02440.1215-0.01280.1149-14.015-3.87372.5551
64.00283.5744.45173.23563.77695.81960.1903-0.017-0.25480.2284-0.086-0.02840.34540.053-0.08930.19520.0118-0.04090.0818-0.02530.1759-10.1574-10.661615.4242
72.341-3.87482.84129.3033-4.14163.6284-0.0625-0.1814-0.20730.47840.21930.6167-0.0325-0.2535-0.11880.14120.01950.00150.2508-0.03060.1917-14.31863.36626.7596
80.64120.8159-0.18195.33242.05392.135-0.1137-0.06920.14130.10560.14450.64240.367-0.0628-0.01860.1917-0.0296-0.06530.15180.00950.2325-17.3456-12.394716.6814
93.65571.93353.1172.44311.36953.93240.248-0.2899-0.09360.1486-0.1812-0.01030.3294-0.2003-0.04960.1827-0.0163-0.05360.12230.00740.143-4.7357-11.00123.0751
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 49 )A10 - 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 106 )A77 - 106
6X-RAY DIFFRACTION6chain 'A' and (resid 107 through 115 )A107 - 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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