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- PDB-3oaf: Structural and Kinetic Data for Antifolate Interactions Against P... -

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Basic information

Entry
Database: PDB / ID: 3oaf
TitleStructural and Kinetic Data for Antifolate Interactions Against Pneumocystis jirovecii, Pneumocystis carinii and Human Dihydrofolate Reductase and Thier Active Site Mutants
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/INHIBITOR / hDHFR inhibitor complexes / OXIDOREDUCTASE-INHIBITOR complex
Function / homology
Function and homology information


regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / folic acid binding / axon regeneration / dihydrofolate metabolic process / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / response to methotrexate / sequence-specific mRNA binding / folic acid binding / axon regeneration / dihydrofolate metabolic process / G1/S-Specific Transcription / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / one-carbon metabolic process / mRNA regulatory element binding translation repressor activity / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / 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
Chem-OAG / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCody, V.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2013
Title: Kinetic and structural analysis for potent antifolate inhibition of Pneumocystis jirovecii, Pneumocystis carinii, and human dihydrofolate reductases and their active-site variants.
Authors: Cody, V. / Pace, J. / Queener, S.F. / Adair, O.O. / Gangjee, A.
History
DepositionAug 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1577
Polymers21,3421
Non-polymers8166
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.128, 84.128, 78.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-249-

HOH

21A-255-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 21341.545 Da / Num. of mol.: 1 / Fragment: human dihydrofolate reductase / Mutation: Q35S, N64F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR, DHFRP1 / Plasmid: pds5 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-OAG / 6-{[(2,5-dichlorophenyl)amino]methyl}pyrido[2,3-d]pyrimidine-2,4-diamine


Mass: 335.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12Cl2N6
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM K2HPO4, 60% saturated Ammonium Sulfate, 3% v/v ethanol, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.975 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 21, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.7→53.3 Å / Num. all: 31164 / Num. obs: 21273 / % possible obs: 93.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.074 / Net I/σ(I): 5.8
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 4 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2222 / Rsym value: 0.43 / % possible all: 66.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0088refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u72

1u72


Resolution: 1.7→42.07 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.647 / SU ML: 0.087 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25304 1090 5.1 %RANDOM
Rwork0.20531 ---
obs0.20767 20183 93.5 %-
all-21273 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.905 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.217 Å
Refinement stepCycle: LAST / Resolution: 1.7→42.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 47 97 1646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221582
X-RAY DIFFRACTIONr_angle_refined_deg2.1832.0092140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8165185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.7324.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.48615285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.279158
X-RAY DIFFRACTIONr_chiral_restr0.2580.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211180
X-RAY DIFFRACTIONr_mcbond_it1.31.5929
X-RAY DIFFRACTIONr_mcangle_it2.14821509
X-RAY DIFFRACTIONr_scbond_it3.7063653
X-RAY DIFFRACTIONr_scangle_it5.4714.5631
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 60 -
Rwork0.341 996 -
obs--62.3 %

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