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- PDB-4or7: Klebsiella pneumoniae dihydrofolate reductase complexed with NADP... -

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Basic information

Entry
Database: PDB / ID: 4or7
TitleKlebsiella pneumoniae dihydrofolate reductase complexed with NADPH and 6-ethyl-5-{3-[3-(pyrimidin-5-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine
ComponentsDihydrofolate reductase
KeywordsOxidoreductase/Oxidoreductase inhibitor / 5 / 6 / 7 / 8-tetrahydrofolate / 8-dihydrofolate / hydride shift / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / Chem-25U / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesKlebsiella pneumoniae CG43 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsLamb, K.M. / Anderson, A.C.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: Crystal Structures of Klebsiella pneumoniae Dihydrofolate Reductase Bound to Propargyl-Linked Antifolates Reveal Features for Potency and Selectivity.
Authors: Lamb, K.M. / Lombardo, M.N. / Alverson, J. / Priestley, N.D. / Wright, D.L. / Anderson, A.C.
History
DepositionFeb 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Data collection
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8873
Polymers18,8131
Non-polymers1,0742
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.161, 61.161, 105.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Dihydrofolate reductase


Mass: 18813.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae CG43 (bacteria) / Gene: folA, D364_00170 / Production host: Escherichia coli (E. coli) / References: UniProt: U5M636, 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-25U / 6-ethyl-5-{3-[3-(pyrimidin-5-yl)phenyl]prop-1-yn-1-yl}pyrimidine-2,4-diamine


Mass: 330.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H18N6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100 mM cacodylate, 125 mM sodium acetate, 25% (w/v) PEG 8000, 11 mM calcium chloride, 11 mM bentaine hydrochloride, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 1.76→37.36 Å / Num. all: 25725 / Num. obs: 25725 / % possible obs: 99.99 % / Observed criterion σ(F): 13.28 / Observed criterion σ(I): 13.28
Reflection shellResolution: 1.76→1.79 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→37.36 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 24.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 1817 7.81 %RANDOM
Rwork0.2103 ---
obs0.2134 23264 99.99 %-
all-23264 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→37.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1324 0 73 233 1630
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061534
X-RAY DIFFRACTIONf_angle_d1.1012109
X-RAY DIFFRACTIONf_dihedral_angle_d15.263567
X-RAY DIFFRACTIONf_chiral_restr0.075215
X-RAY DIFFRACTIONf_plane_restr0.004275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.80760.30881390.27531610X-RAY DIFFRACTION100
1.8076-1.86080.28151400.25831629X-RAY DIFFRACTION100
1.8608-1.92090.30261360.25281610X-RAY DIFFRACTION100
1.9209-1.98950.30381370.24711637X-RAY DIFFRACTION100
1.9895-2.06920.2771360.24171618X-RAY DIFFRACTION100
2.0692-2.16330.26381380.24211638X-RAY DIFFRACTION100
2.1633-2.27740.31141370.22621645X-RAY DIFFRACTION100
2.2774-2.420.29441370.22121627X-RAY DIFFRACTION100
2.42-2.60680.29181380.22761646X-RAY DIFFRACTION100
2.6068-2.86910.24721390.21331650X-RAY DIFFRACTION100
2.8691-3.2840.23671410.20441671X-RAY DIFFRACTION100
3.284-4.13670.20771450.17261691X-RAY DIFFRACTION100
4.1367-37.37160.1841540.16321775X-RAY DIFFRACTION100

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