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- PDB-2cvy: Structures of Yeast Ribonucleotide Reductase I -

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Basic information

Entry
Database: PDB / ID: 2cvy
TitleStructures of Yeast Ribonucleotide Reductase I
Components
  • 9-per peptide from Ribonucleoside-diphosphate reductase small chain 1
  • Ribonucleoside-diphosphate reductase large chain 1
KeywordsOXIDOREDUCTASE / Eukaryotic / Ribonucleotide Reductase / dNTP Regulation
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 / ferrous iron binding / molecular adaptor activity / protein heterodimerization activity / nucleotide binding / zinc ion binding ...Interconversion of nucleotide di- and triphosphates / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / ferrous iron binding / molecular adaptor activity / protein heterodimerization activity / nucleotide binding / zinc ion 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 / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / Ribonucleoside-diphosphate reductase small chain 1 / Ribonucleoside-diphosphate reductase large chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsXu, H. / Faber, C. / Uchiki, T. / Fairman, J.W. / Racca, J. / Dealwis, C.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structures of eukaryotic ribonucleotide reductase I provide insights into dNTP regulation
Authors: Xu, H. / Faber, C. / Uchiki, T. / Fairman, J.W. / Racca, J. / Dealwis, C.
History
DepositionJun 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: 9-per peptide from Ribonucleoside-diphosphate reductase small chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,2274
Polymers100,7202
Non-polymers5062
Water1,33374
1
A: Ribonucleoside-diphosphate reductase large chain 1
B: 9-per peptide from Ribonucleoside-diphosphate reductase small chain 1
hetero molecules

A: Ribonucleoside-diphosphate reductase large chain 1
B: 9-per peptide from Ribonucleoside-diphosphate reductase small chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,4538
Polymers201,4404
Non-polymers1,0134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Unit cell
Length a, b, c (Å)108.062, 117.590, 64.216
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe second part of the active biological dimer assembly is generated by the two fold axis: -x, -y+1, z.

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Components

#1: Protein Ribonucleoside-diphosphate reductase large chain 1 / Ribonucleotide reductase I


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 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P21524, ribonucleoside-diphosphate reductase
#2: Protein/peptide 9-per peptide from Ribonucleoside-diphosphate reductase small chain 1 / RNR2 C-terminal 9 mer peptide


Mass: 1047.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemical synthesized
References: UniProt: P09938, ribonucleoside-diphosphate reductase
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 37.3 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: PEG 3350, sodium acetate, ammonium sulfate, pH 6.5, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 32238 / Num. obs: 32238 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 11.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5 % / Rmerge(I) obs: 0.472 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3131 / Rsym value: 0.472 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure

Resolution: 2.4→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.9 / SU B: 7.851 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.45 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3222 10 %RANDOM
Rwork0.21788 ---
obs0.22242 28970 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.9 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5194 0 30 74 5298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225347
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9487245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.064251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1531
X-RAY DIFFRACTIONr_chiral_restr0.2784
X-RAY DIFFRACTIONr_gen_planes_refined0.024049
X-RAY DIFFRACTIONr_nbd_refined0.22556
X-RAY DIFFRACTIONr_nbtor_refined0.23613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.23
X-RAY DIFFRACTIONr_mcbond_it1.53302
X-RAY DIFFRACTIONr_mcangle_it25206
X-RAY DIFFRACTIONr_scbond_it32352
X-RAY DIFFRACTIONr_scangle_it4.52039
LS refinement shellResolution: 2.396→2.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 221 -
Rwork0.253 2044 -
obs--94.3 %

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