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- PDB-1smq: Structure of the Ribonucleotide Reductase Rnr2 Homodimer from Sac... -

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Basic information

Entry
Database: PDB / ID: 1smq
TitleStructure of the Ribonucleotide Reductase Rnr2 Homodimer from Saccharomyces cerevisiae
ComponentsRibonucleoside-diphosphate reductase small chain 1
KeywordsOXIDOREDUCTASE
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 / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase small chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsSommerhalter, M. / Voegtli, W.C. / Perlstein, D.L. / Ge, J. / Stubbe, J. / Rosenzweig, A.C.
CitationJournal: Biochemistry / Year: 2004
Title: Structures of the yeast ribonucleotide reductase Rnr2 and Rnr4 homodimers.
Authors: Sommerhalter, M. / Voegtli, W.C. / Perlstein, D.L. / Ge, J. / Stubbe, J. / Rosenzweig, A.C.
History
DepositionMar 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 small chain 1
B: Ribonucleoside-diphosphate reductase small chain 1
C: Ribonucleoside-diphosphate reductase small chain 1
D: Ribonucleoside-diphosphate reductase small chain 1


Theoretical massNumber of molelcules
Total (without water)184,8294
Polymers184,8294
Non-polymers00
Water00
1
A: Ribonucleoside-diphosphate reductase small chain 1
D: Ribonucleoside-diphosphate reductase small chain 1


Theoretical massNumber of molelcules
Total (without water)92,4152
Polymers92,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-16 kcal/mol
Surface area29070 Å2
MethodPISA
2
B: Ribonucleoside-diphosphate reductase small chain 1
C: Ribonucleoside-diphosphate reductase small chain 1


Theoretical massNumber of molelcules
Total (without water)92,4152
Polymers92,4152
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-16 kcal/mol
Surface area29190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.670, 79.570, 88.050
Angle α, β, γ (deg.)83.47, 83.45, 70.79
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Ribonucleoside-diphosphate reductase small chain 1 / Ribonucleotide reductase small subunit


Mass: 46207.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RNR2, YJL026W, J1271 / Production host: Escherichia coli (E. coli)
References: UniProt: P09938, ribonucleoside-diphosphate reductase

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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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Succinate, PEG3350, lithium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→87 Å / Num. obs: 168766 / % possible obs: 94.6 % / Rsym value: 0.059 / Net I/σ(I): 7.2
Reflection shellResolution: 3.1→3.27 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.294 / % possible all: 96

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1JK0 subunit Y2

1jk0


Resolution: 3.1→25 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.303 3447 random
Rwork0.272 --
obs-34663 -
Refinement stepCycle: LAST / Resolution: 3.1→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10690 0 0 0 10690
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_bond_d0.008

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