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- PDB-2zlf: The Structural Basis for Peptidomimetic Inhibition of Eukaryotic ... -

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Basic information

Entry
Database: PDB / ID: 2zlf
TitleThe Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase
Components
  • FTLDADF
  • Ribonucleoside-diphosphate reductase large chain 1
KeywordsOXIDOREDUCTASE / peptidomimetic inhibition eukaryotic ribonucleotide reductase / Allosteric enzyme / ATP-binding / Cytoplasm / DNA replication / Nucleotide-binding / Phosphoprotein
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / nucleotide binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal ...ATP-cone domain / ATP cone domain / ATP-cone domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / Ribonucleotide reductase R1 subunit, N-terminal / Ribonucleotide reductase large subunit, N-terminal / Ribonucleotide reductase, all-alpha domain / Ribonucleotide reductase large subunit, C-terminal / Ribonucleotide reductase, barrel domain / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase large chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsXu, H. / Fairman, J.W. / Wijerathna, S.R. / LaMacchia, J. / Kreischer, N.R. / Helmbrecht, E. / Cooperman, B.S. / Dealwis, C.
CitationJournal: J.Med.Chem. / Year: 2008
Title: The Structural Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase: A Conformationally Flexible Pharmacophore
Authors: Xu, H. / Fairman, J.W. / Wijerathna, S.R. / Kreischer, N.R. / LaMacchia, J. / Helmbrecht, E. / Cooperman, B.S. / Dealwis, C.
History
DepositionApr 9, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Ribonucleoside-diphosphate reductase large chain 1
B: FTLDADF


Theoretical massNumber of molelcules
Total (without water)100,5012
Polymers100,5012
Non-polymers00
Water1,29772
1
A: Ribonucleoside-diphosphate reductase large chain 1
B: FTLDADF

A: Ribonucleoside-diphosphate reductase large chain 1
B: FTLDADF


Theoretical massNumber of molelcules
Total (without water)201,0024
Polymers201,0024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4810 Å2
ΔGint-31.1 kcal/mol
Surface area48760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.948, 116.999, 63.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonucleoside-diphosphate reductase large chain 1 / Ribonucleotide reductase large subunit 1 / RNR1 / Ribonucleotide reductase R1 subunit 1


Mass: 99672.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PWJ751-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21524, ribonucleoside-diphosphate reductase
#2: Protein/peptide FTLDADF


Mass: 827.878 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.01 Å3/Da / Density % sol: 38.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Hepes, 20-25% PEG 3350, 0.2M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 1, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 24929 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 6.6 % / Rsym value: 0.081 / Net I/σ(I): 21.5
Reflection shellResolution: 2.589→2.656 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.459 / % possible all: 82.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CVX

2cvx


Resolution: 2.59→49.75 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.92 / Cross valid method: THROUGHOUT / ESU R: 0.868 / ESU R Free: 0.322 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25143 1262 5.1 %RANDOM
Rwork0.19249 ---
obs0.19554 23611 96.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.936 Å2
Baniso -1Baniso -2Baniso -3
1--3.11 Å20 Å20 Å2
2---2.67 Å20 Å2
3---5.78 Å2
Refinement stepCycle: LAST / Resolution: 2.59→49.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5354 0 0 72 5426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0225477
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9427415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4945667
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55724.062256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23615954
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2821533
X-RAY DIFFRACTIONr_chiral_restr0.10.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024157
X-RAY DIFFRACTIONr_nbd_refined0.2510.22920
X-RAY DIFFRACTIONr_nbtor_refined0.3340.23779
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2208
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.27
X-RAY DIFFRACTIONr_mcbond_it3.2661.53336
X-RAY DIFFRACTIONr_mcangle_it4.62325387
X-RAY DIFFRACTIONr_scbond_it4.91632141
X-RAY DIFFRACTIONr_scangle_it6.5774.52028
LS refinement shellResolution: 2.589→2.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 79 -
Rwork0.253 1388 -
obs--77.78 %

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