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- PDB-7ese: The Crystal Structure of human DHFR from Biortus -

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Basic information

Entry
Database: PDB / ID: 7ese
TitleThe Crystal Structure of human DHFR from Biortus
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / catalytic activity / dihydrofolate reductase activity / oxidoreductase activity
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 / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process ...regulation of removal of superoxide radicals / tetrahydrobiopterin biosynthetic process / Metabolism of folate and pterines / tetrahydrofolate metabolic process / sequence-specific mRNA binding / response to methotrexate / axon regeneration / folic acid binding / G1/S-Specific Transcription / dihydrofolate metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / 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 / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsWang, F. / Cheng, W. / Xu, C. / Qi, J. / Bao, X. / Miao, Q.
CitationJournal: To Be Published
Title: The Crystal Structure of human DHFR from Biortus
Authors: Wang, F. / Cheng, W. / Xu, C. / Qi, J. / Bao, X. / Miao, Q.
History
DepositionMay 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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)24,6793
Polymers23,4941
Non-polymers1,1852
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-3 kcal/mol
Surface area9510 Å2
Unit cell
Length a, b, c (Å)61.569, 61.569, 94.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-81-

LYS

21A-363-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 23493.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHFR / Production host: Escherichia coli (E. coli) / References: UniProt: P00374, 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-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.15M KBr, 30% PEGMME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.5212 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5212 Å / Relative weight: 1
ReflectionResolution: 1.85→47.03 Å / Num. obs: 16095 / % possible obs: 100 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 15.9
Reflection shellResolution: 1.85→1.89 Å / Rmerge(I) obs: 1.086 / Num. unique obs: 946

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOZ

1boz


Resolution: 1.85→39.541 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.414 / SU ML: 0.155 / Cross valid method: FREE R-VALUE / ESU R: 0.199 / ESU R Free: 0.177
RfactorNum. reflection% reflection
Rfree0.285 791 4.957 %
Rwork0.2405 15165 -
all0.243 --
obs-15956 99.352 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.357 Å2
Baniso -1Baniso -2Baniso -3
1-1.431 Å2-0 Å2-0 Å2
2--1.431 Å2-0 Å2
3----2.861 Å2
Refinement stepCycle: LAST / Resolution: 1.85→39.541 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1495 0 80 77 1652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131616
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171478
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.7272192
X-RAY DIFFRACTIONr_angle_other_deg1.1361.6163451
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0485184
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83323.29179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2815285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.944158
X-RAY DIFFRACTIONr_chiral_restr0.0560.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
X-RAY DIFFRACTIONr_nbd_refined0.1950.2291
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21452
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2745
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2713
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.070.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.223
X-RAY DIFFRACTIONr_nbd_other0.2210.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.27
X-RAY DIFFRACTIONr_mcbond_it1.5873.343742
X-RAY DIFFRACTIONr_mcbond_other1.5863.345740
X-RAY DIFFRACTIONr_mcangle_it2.5855.004924
X-RAY DIFFRACTIONr_mcangle_other2.5845.004924
X-RAY DIFFRACTIONr_scbond_it1.613.527873
X-RAY DIFFRACTIONr_scbond_other1.6093.525874
X-RAY DIFFRACTIONr_scangle_it2.6935.211266
X-RAY DIFFRACTIONr_scangle_other2.6925.2081267
X-RAY DIFFRACTIONr_lrange_it4.32937.1371798
X-RAY DIFFRACTIONr_lrange_other4.28937.0321787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.8980.447600.3871049X-RAY DIFFRACTION96.8559
1.898-1.950.389590.3561045X-RAY DIFFRACTION98.6595
1.95-2.0060.323490.3231052X-RAY DIFFRACTION99.458
2.006-2.0680.369640.324995X-RAY DIFFRACTION99.5301
2.068-2.1360.345450.29997X-RAY DIFFRACTION99.6176
2.136-2.2110.401480.299960X-RAY DIFFRACTION99.6047
2.211-2.2940.35500.292914X-RAY DIFFRACTION98.6694
2.294-2.3870.317460.262885X-RAY DIFFRACTION99.4658
2.387-2.4930.367440.265858X-RAY DIFFRACTION99.5585
2.493-2.6150.341440.256829X-RAY DIFFRACTION100
2.615-2.7560.329460.26771X-RAY DIFFRACTION99.7558
2.756-2.9220.259350.25752X-RAY DIFFRACTION99.7465
2.922-3.1230.447270.245718X-RAY DIFFRACTION99.3333
3.123-3.3730.28350.225653X-RAY DIFFRACTION100
3.373-3.6930.229320.216608X-RAY DIFFRACTION100
3.693-4.1260.235310.199571X-RAY DIFFRACTION100
4.126-4.7590.24290.18503X-RAY DIFFRACTION100
4.759-5.8170.189180.182433X-RAY DIFFRACTION100
5.817-8.1740.222150.197353X-RAY DIFFRACTION99.729
8.174-39.5410.153140.153219X-RAY DIFFRACTION99.1489

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