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- PDB-4osg: Klebsiella pneumoniae complexed with NADPH and 6-ethyl-5-[(3R)-3-... -

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Basic information

Entry
Database: PDB / ID: 4osg
TitleKlebsiella pneumoniae complexed with NADPH and 6-ethyl-5-[(3R)-3-[3-methoxyl-5-(pyridine-4-yl)phenyl]but-1-yn-1-yl]pyrimidine-2,4-diamine (UCP1006)
ComponentsDihydrofolate reductase
KeywordsOxidoreductase/Oxidoreductase inhibitor / Oxidoreductase / hydride shift / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-06U / CACODYLATE ION / ETHANOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / :
Similarity search - Component
Biological speciesKlebsiella pneumoniae CG43 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 12, 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
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,36822
Polymers75,2534
Non-polymers5,11618
Water23413
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9764
Polymers18,8131
Non-polymers1,1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1025
Polymers18,8131
Non-polymers1,2894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1477
Polymers18,8131
Non-polymers1,3346
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1436
Polymers18,8131
Non-polymers1,3295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.120, 74.210, 82.530
Angle α, β, γ (deg.)67.94, 77.70, 75.92
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Dihydrofolate reductase /


Mass: 18813.152 Da / Num. of mol.: 4
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

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Non-polymers , 8 types, 31 molecules

#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-06U / 6-ethyl-5-{(3R)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1-yl}pyrimidine-2,4-diamine


Mass: 373.451 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23N5O
#4: Chemical ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.62 Å3/Da / Density % sol: 53.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 100 mM cacodylate pH7.4, 125 mM sodium acetate, 25% (w/v) PEG 8000, 11 mM calcium chloride, 11 mM bentaine hydrochloride, 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 4 / Detector: CCD / Date: Nov 16, 2013
RadiationMonochromator: A KOHZU double crystal monochromator with a sagittally focused second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→39.27 Å / Num. all: 20988 / Num. obs: 19813 / % possible obs: 94.4 % / Observed criterion σ(F): 13.4 / Observed criterion σ(I): 13.4 / Redundancy: 1.67 % / Rmerge(I) obs: 0.049 / Rsym value: 0.07 / Net I/σ(I): 13.4
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.468 / % possible all: 95.1

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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: 2.7→39.27 Å / σ(F): 2.7 / Phase error: 35.41 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2483 2106 10.66 %RANDOM
Rwork0.239 ---
all-19813 --
obs-19765 94.18 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→39.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5056 0 330 13 5399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075528
X-RAY DIFFRACTIONf_angle_d1.2457546
X-RAY DIFFRACTIONf_dihedral_angle_d14.1442028
X-RAY DIFFRACTIONf_chiral_restr0.051788
X-RAY DIFFRACTIONf_plane_restr0.005948
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.76750.48011420.40911323X-RAY DIFFRACTION86
2.7675-2.84230.49291380.44221256X-RAY DIFFRACTION85
2.8423-2.92590.40431340.39181248X-RAY DIFFRACTION84
2.9259-3.02030.38621430.40121303X-RAY DIFFRACTION86
3.0203-3.12820.40381450.33641257X-RAY DIFFRACTION85
3.1282-3.25340.34131400.30521292X-RAY DIFFRACTION85
3.2534-3.40140.321400.30681251X-RAY DIFFRACTION85
3.4014-3.58060.27861410.25511311X-RAY DIFFRACTION86
3.5806-3.80480.27421420.26221234X-RAY DIFFRACTION85
3.8048-4.09830.22621480.23141296X-RAY DIFFRACTION85
4.0983-4.51020.21031430.1811289X-RAY DIFFRACTION85
4.5102-5.16160.16141450.17341268X-RAY DIFFRACTION85
5.1616-6.49830.24081410.19151227X-RAY DIFFRACTION84
6.4983-39.27460.1641400.1791227X-RAY DIFFRACTION81

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