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- PDB-4kl9: Crystal structure of dihydrofolate reductase from Mycobacterium t... -

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Basic information

Entry
Database: PDB / ID: 4kl9
TitleCrystal structure of dihydrofolate reductase from Mycobacterium tuberculosis in the space group C2
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / reductase
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, 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-NDP / Dihydrofolate reductase / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsDias, M.V.B. / Tyrakis, P. / Blundell, T.L.
CitationJournal: Structure / Year: 2014
Title: Mycobacterium tuberculosis Dihydrofolate Reductase Reveals Two Conformational States and a Possible Low Affinity Mechanism to Antifolate Drugs.
Authors: Dias, M.V. / Tyrakis, P. / Domingues, R.R. / Paes Leme, A.F. / Blundell, T.L.
History
DepositionMay 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)20,9043
Polymers19,8321
Non-polymers1,0722
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.580, 73.590, 36.830
Angle α, β, γ (deg.)90.000, 98.770, 90.000
Int Tables number5
Space group name H-MC121

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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) / Strain: H37Rv / Gene: dfrA, folA, MT2833, MTV002.28c, Rv2763c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A546, UniProt: P9WNX1*PLUS, dihydrofolate reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.28 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Mes, PEGMME 2000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9716 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 8, 2009
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9716 Å / Relative weight: 1
ReflectionResolution: 1.39→49.457 Å / Num. all: 36064 / Num. obs: 36064 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.038 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.39-1.463.70.5861.31929752500.586100
1.46-1.553.70.342.21848649690.34100
1.55-1.663.70.23.81745846720.2100
1.66-1.793.80.1335.51645743780.133100
1.79-1.963.80.0768.81511339920.076100
1.96-2.193.80.04514.61380336350.045100
2.19-2.533.80.039151220731960.039100
2.53-3.13.80.04312.81046827380.043100
3.1-4.383.80.02522.7798020850.02599.8
4.38-24.7293.60.0225.7418411490.0297

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
MOSFLMdata reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.39→23.03 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.275 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 1799 5 %RANDOM
Rwork0.1546 ---
obs0.157 36063 99.87 %-
all-36064 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.88 Å2 / Biso mean: 26.6536 Å2 / Biso min: 10.25 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.39→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1249 0 70 178 1497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021360
X-RAY DIFFRACTIONr_angle_refined_deg2.3882.0091852
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8385161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64621.35659
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88915202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1371517
X-RAY DIFFRACTIONr_chiral_restr0.3480.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211027
X-RAY DIFFRACTIONr_rigid_bond_restr8.68531360
X-RAY DIFFRACTIONr_sphericity_free33.769569
X-RAY DIFFRACTIONr_sphericity_bonded17.6751434
LS refinement shellResolution: 1.39→1.422 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 126 -
Rwork0.279 2478 -
all-2604 -
obs--100 %

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