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- PDB-3f91: Structural Data for Human Active Site Mutant Enzyme Complexes -

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Basic information

Entry
Database: PDB / ID: 3f91
TitleStructural 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 / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / dihydrofolate metabolic process / axon regeneration / folic acid binding / G1/S-Specific Transcription / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / NADPH binding / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / tetrahydrofolate biosynthetic process / mRNA regulatory element binding translation repressor activity / positive regulation of nitric-oxide synthase activity / one-carbon metabolic process / NADP binding / negative regulation of translation / mRNA binding / mitochondrion / 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-DH1 / Chem-NDP / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.3Oct 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 29, 2023Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_name

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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)22,7575
Polymers21,4731
Non-polymers1,2844
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.629, 84.629, 77.920
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: 21472.742 Da / Num. of mol.: 1 / Mutation: Q35S, N64F
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 / Nicotinamide adenine dinucleotide phosphate


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


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


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM potassium phosphate, pH 6.9, 60% ammonium sulfate, 3% ethanol, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 26, 2008 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.63→26.69 Å / Num. obs: 20592 / % possible obs: 79.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 3.9 % / Biso Wilson estimate: 34.56 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.026 / Net I/σ(I): 28.1
Reflection shellResolution: 1.63→1.72 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.075 / Mean I/σ(I) obs: 9 / Num. unique all: 755 / Rsym value: 0.064 / % possible all: 20

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1u72

1u72


Resolution: 1.9→26.7 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.893 / SU B: 3.024 / SU ML: 0.093 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / ESU R: 0.158 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23756 864 5.3 %RANDOM
Rwork0.17905 ---
obs0.18211 15476 99.58 %-
all-15476 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.495 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.189 Å
Refinement stepCycle: LAST / Resolution: 1.9→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 83 168 1753
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221624
X-RAY DIFFRACTIONr_angle_refined_deg2.062.0412202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.3924.57170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.281158
X-RAY DIFFRACTIONr_chiral_restr0.1480.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021203
X-RAY DIFFRACTIONr_nbd_refined0.2120.2716
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21057
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2155
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.217
X-RAY DIFFRACTIONr_mcbond_it1.0071.5975
X-RAY DIFFRACTIONr_mcangle_it1.44721509
X-RAY DIFFRACTIONr_scbond_it2.4343773
X-RAY DIFFRACTIONr_scangle_it3.4774.5693
LS refinement shellResolution: 1.9→1.95 Å / Rfactor Rfree error: 0.13 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 56 -
Rwork0.196 1095 -
obs-230 94.42 %

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