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- PDB-1jk0: Ribonucleotide reductase Y2Y4 heterodimer -

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Basic information

Entry
Database: PDB / ID: 1jk0
TitleRibonucleotide reductase Y2Y4 heterodimer
Components
  • ribonucleoside-diphosphate reductase small chain 1
  • ribonucleoside-diphosphate reductase small chain 2
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / R2
Function / homology
Function and homology information


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 / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
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, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase small chain 1 / Ribonucleoside-diphosphate reductase small chain 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsVoegtli, W.C. / Perlstein, D.L. / Ge, J. / Stubbe, J. / Rosenzweig, A.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structure of the yeast ribonucleotide reductase Y2Y4 heterodimer.
Authors: Voegtli, W.C. / Ge, J. / Perlstein, D.L. / Stubbe, J. / Rosenzweig, A.C.
History
DepositionJul 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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: ribonucleoside-diphosphate reductase small chain 1
B: ribonucleoside-diphosphate reductase small chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5473
Polymers88,4812
Non-polymers651
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-15 kcal/mol
Surface area27380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.900, 93.000, 97.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsBiological assembly is a heterodimer of monomers of Y2 and Y4

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Components

#1: Protein ribonucleoside-diphosphate reductase small chain 1 / RNR Y2


Mass: 48378.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNR2 / Plasmid: pET-14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P09938, ribonucleoside-diphosphate reductase
#2: Protein ribonucleoside-diphosphate reductase small chain 2 / RNR Y4


Mass: 40102.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNR4 / Plasmid: pET-14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P49723, ribonucleoside-diphosphate reductase
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 293 K / Method: sandwich drop / pH: 4.9
Details: 100 mM acetate, 14% w/v polyethyleneglycol 4000, 200 mM NaCl, pH 4.9, sandwich drop, temperature 293K
Crystal grow
*PLUS
pH: 5.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
150 mMTris11
24 mg/mlprotein11
3100 mMacetate12
414 %(w/v)PEG400012
5200 mM12NaCl

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.946 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 30, 2000
RadiationMonochromator: Si double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.946 Å / Relative weight: 1
ReflectionResolution: 2.8→9 Å / Num. all: 20545 / Num. obs: 19844 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 17.7
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1530 / Rsym value: 0.286 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 15 Å / Num. obs: 20645 / % possible obs: 99.9 % / Num. measured all: 65155 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Lowest resolution: 2.85 Å / % possible obs: 99.8 % / Rmerge(I) obs: 0.285

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Processing

Software
NameVersionClassification
CNSderived MIR phases with sites found in SOLVErefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSDERIVED MIR PHASES WITH SITES FOUND IN SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→9 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 564143.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 1453 7.4 %RANDOM
Rwork0.243 ---
all0.243 20545 --
obs0.243 19752 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5531 Å2 / ksol: 0.443753 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.09 Å20 Å20 Å2
2---2.64 Å20 Å2
3---8.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.8→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4944 0 1 58 5003
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d19.6
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 236 8 %
Rwork0.317 2714 -
obs--87.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3TOPPER_ION.PARAMTOPPER_ION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 7.4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 46.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
LS refinement shell
*PLUS
Rfactor Rfree: 0.374 / % reflection Rfree: 8 % / Rfactor Rwork: 0.317

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