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- PDB-3s8b: Structure of Yeast Ribonucleotide Reductase 1 with AMPPNP and CDP -

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Basic information

Entry
Database: PDB / ID: 3s8b
TitleStructure of Yeast Ribonucleotide Reductase 1 with AMPPNP and CDP
ComponentsRibonucleoside-diphosphate reductase large chain 1
KeywordsOXIDOREDUCTASE / dNTP regulation / allostery
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / nucleotide binding / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Ribonucleotide reductase, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / 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, class I , alpha subunit / Ribonucleotide reductase large subunit signature. / Ribonucleoside-diphosphate reductase large subunit / ATP-cone domain / ATP cone domain / ATP-cone domain profile. / 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 / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / CYTIDINE-5'-DIPHOSPHATE / Ribonucleoside-diphosphate reductase large chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous / Resolution: 2.8 Å
AuthorsAhmad, M.F. / Kaushal, P.S. / Wan, Q. / Wijeratna, S.R. / Huang, M. / Dealwis, C.D.
CitationJournal: To be Published
Title: Structural and biochemical basis of lethal mutant R293A of yeast ribonucleotide reductase
Authors: Ahmad, M.F. / Kaushal, P.S. / Wan, Q. / Wijeratna, S.R. / Huang, M. / Dealwis, C.D.
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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)100,6074
Polymers99,6731
Non-polymers9343
Water75742
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)201,2138
Polymers199,3462
Non-polymers1,8676
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2900 Å2
ΔGint-17 kcal/mol
Surface area48830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.869, 117.567, 64.967
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 R1 subunit 1 / Ribonucleotide reductase large subunit 1


Mass: 99672.984 Da / Num. of mol.: 1 / Fragment: Ribonucleotide Reductase 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: CRT7, RIR1, RNR1, Saccharomyces, SDS12, YER070W / Plasmid: pWJ751-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21524, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE / Cytidine diphosphate


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 20-25% PEG 3350, 0.1 M HEPES, 0.1 M sodium chloride, pH 7.0, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 26, 2011
RadiationMonochromator: single crystal side- bounce monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.8→49.03 Å / Num. all: 21212 / Num. obs: 18651 / % possible obs: 98.76 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 12.5
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.8 / % possible all: 97

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: Isomorphous / Resolution: 2.8→49.03 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.959 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25027 2083 10 %RANDOM
Rwork0.20865 ---
obs0.21289 18651 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.421 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5223 0 57 42 5322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225393
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.9667325
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15324.153248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.13515903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8371531
X-RAY DIFFRACTIONr_chiral_restr0.0940.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024084
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22441
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2178
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0250.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0280.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.53351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92625290
X-RAY DIFFRACTIONr_scbond_it1.29632328
X-RAY DIFFRACTIONr_scangle_it1.8974.52035
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 143 -
Rwork0.268 1373 -
obs--99.54 %

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