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- PDB-3f8y: Correlations of Human Dihydrofolate Reductase with Structural Dat... -

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Basic information

Entry
Database: PDB / ID: 3f8y
TitleCorrelations of Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / active site mutants ligand complex DHFR / NADP / One-carbon metabolism
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-DH1 / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsCody, V. / Pace, J. / Makin, J. / Piraino, J. / Queener, S.F. / Rosowsky, A.
CitationJournal: Biochemistry / Year: 2009
Title: Correlations of Inhibitor Kinetics for Pneumocystis jirovecii and Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes.
Authors: Cody, V. / Pace, J. / Makin, J. / Piraino, J. / Queener, S.F. / Rosowsky, A.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 30, 2014Group: Data collection
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,7665
Polymers21,4821
Non-polymers1,2844
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.294, 84.294, 78.117
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Dihydrofolate reductase


Mass: 21481.773 Da / Num. of mol.: 1 / Mutation: Q35K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR, DHFRP1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P00374, dihydrofolate reductase
#2: Chemical ChemComp-DH1 / 2,4-DIAMINO-5-[2-METHOXY-5-(4-CARBOXYBUTYLOXY)BENZYL]PYRIMIDINE


Mass: 346.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22N4O4
#3: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 50.83 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM potassium phosphate, pH 6.9, 30% ammonium sulfate, 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 6, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→53.3 Å / Num. obs: 50420 / % possible obs: 79.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.046 / Net I/σ(I): 16.7
Reflection shellResolution: 1.45→1.53 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 0.9 / Num. unique all: 1654 / Rsym value: 0.562 / % possible all: 98.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u72

1u72


Resolution: 1.45→26.67 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 1.12 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.076 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22762 1817 5 %RANDOM
Rwork0.18978 ---
all0.1898 34546 --
obs0.1917 34542 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.698 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: 0.159 Å
Refinement stepCycle: LAST / Resolution: 1.45→26.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 83 372 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221623
X-RAY DIFFRACTIONr_angle_refined_deg1.8022.0422200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8985185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29824.71470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63115288
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.798158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021200
X-RAY DIFFRACTIONr_nbd_refined0.2190.2826
X-RAY DIFFRACTIONr_nbtor_refined0.310.21083
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2343
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.239
X-RAY DIFFRACTIONr_mcbond_it0.8231.5962
X-RAY DIFFRACTIONr_mcangle_it1.36521509
X-RAY DIFFRACTIONr_scbond_it1.9493766
X-RAY DIFFRACTIONr_scangle_it2.9774.5691
LS refinement shellResolution: 1.45→1.488 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 138 -
Rwork0.23 2543 -
obs-16037 98.31 %

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