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- PDB-2zlg: The Structual Basis for Peptidomimetic Inhibition of Eukaryotic R... -

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Basic information

Entry
Database: PDB / ID: 2zlg
TitleThe Structual Basis for Peptidomimetic Inhibition of Eukaryotic Ribonucleotide Reductase
ComponentsRibonucleoside-diphosphate reductase large chain 1
KeywordsOXIDOREDUCTASE / peptidomimetic inhibition eukaryotic ribonucleotide reductase / Allosteric enzyme / ATP-binding / 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
Chem-MRT / Ribonucleoside-diphosphate reductase large chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.52 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: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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: Ribonucleoside-diphosphate reductase large chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8884
Polymers99,6731
Non-polymers1,2153
Water1,65792
1
A: Ribonucleoside-diphosphate reductase large chain 1
hetero molecules

A: Ribonucleoside-diphosphate reductase large chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,7778
Polymers199,3462
Non-polymers2,4316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3320 Å2
ΔGint-18 kcal/mol
Surface area50260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.789, 116.565, 63.641
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: Chemical ChemComp-MRT / (5R,9S,12S,15S,18S,21S)-21-benzyl-12,18-bis(carboxymethyl)-15-cyclohexyl-1-(9H-fluoren-9-yl)-4-methyl-9-(2-methylpropyl)-3,6,10,13,16,19-hexaoxo-5-phenyl-2-oxa-4,8,11,14,17,20-hexaazadocosan-22-oic acid


Mass: 1031.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C56H66N6O13
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsMRT IS MAMMALIAN R2 C-TERMINAL P6 PEPTIDOMIMETIC

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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: 38.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Hepes, 20-25% PEG3350, 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: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2.52→79.06 Å / Num. obs: 27055 / % possible obs: 98.3 % / Redundancy: 4.7 % / Rsym value: 0.074 / Net I/σ(I): 18.8
Reflection shellResolution: 2.522→2.587 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.461 / % possible all: 92.4

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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: 2.52→49.6 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.906 / Cross valid method: THROUGHOUT / ESU R: 0.661 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2919 1359 5 %RANDOM
Rwork0.21553 ---
obs0.21916 25564 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.129 Å2
Baniso -1Baniso -2Baniso -3
1--5.59 Å20 Å20 Å2
2---2.7 Å20 Å2
3---8.29 Å2
Refinement stepCycle: LAST / Resolution: 2.52→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 87 92 5407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225457
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9637388
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1475651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.424.032248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.31915935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6861532
X-RAY DIFFRACTIONr_chiral_restr0.0880.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024130
X-RAY DIFFRACTIONr_nbd_refined0.2560.22867
X-RAY DIFFRACTIONr_nbtor_refined0.3330.23804
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2187
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.240.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.27
X-RAY DIFFRACTIONr_mcbond_it3.8451.53262
X-RAY DIFFRACTIONr_mcangle_it5.17625271
X-RAY DIFFRACTIONr_scbond_it5.41232195
X-RAY DIFFRACTIONr_scangle_it7.14.52117
LS refinement shellResolution: 2.522→2.587 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 90 -
Rwork0.342 1473 -
obs--78.11 %

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