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- PDB-3fs6: Correlations of Inhibitor Kinetics for Pneumocystis jirovecii and... -

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Basic information

Entry
Database: PDB / ID: 3fs6
TitleCorrelations of Inhibitor Kinetics for Pneumocystis jirovecii and Human Dihydrofolate Reductase with Structural Data for Human Active Site Mutant Enzyme Complexes
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / human wild type DHFR active site inhibitors / 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 / folic acid metabolic 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 (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: 1.23 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
DepositionJan 9, 2009Deposition 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 1.3Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)22,5733
Polymers21,4811
Non-polymers1,0922
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.098, 84.098, 78.054
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: 21480.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: pDS5 / Plasmid: pDS5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 100 mM K2PO4, pH 6.9, 60% sat. AS with 3% ethanol, 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: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 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: 1.23→53.2 Å / Num. all: 59797 / Num. obs: 56766 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.1 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.02 / Net I/σ(I): 20.8
Reflection shellResolution: 1.23→1.33 Å / Redundancy: 10.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.5 / Num. unique all: 939 / Rsym value: 0.324 / % possible all: 100

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Processing

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

1u72


Resolution: 1.23→34.4 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.937 / SU B: 0.767 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26019 3022 5.1 %RANDOM
Rwork0.24494 ---
obs0.24572 56758 99.98 %-
all-59797 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.036 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.178 Å / Luzzati d res low obs: 1.23 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 1.23→34.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1502 0 73 67 1642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221615
X-RAY DIFFRACTIONr_angle_refined_deg1.5772.0352189
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7595185
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43724.78971
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93215286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.923158
X-RAY DIFFRACTIONr_chiral_restr0.1260.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021204
X-RAY DIFFRACTIONr_nbd_refined0.1980.2674
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21076
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.278
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.211
X-RAY DIFFRACTIONr_mcbond_it0.8611.5964
X-RAY DIFFRACTIONr_mcangle_it1.30721509
X-RAY DIFFRACTIONr_scbond_it1.9543759
X-RAY DIFFRACTIONr_scangle_it2.7244.5680
LS refinement shellResolution: 1.23→1.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 229 -
Rwork0.335 4195 -
obs--100 %

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