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- PDB-6y2n: Crystal structure of ribonucleotide reductase R2 subunit solved b... -

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Basic information

Entry
Database: PDB / ID: 6y2n
TitleCrystal structure of ribonucleotide reductase R2 subunit solved by serial synchrotron crystallography
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT / MN/FE COFACTOR / METALLOPROTEIN OXIDOREDUCTASE / FERRITIN-LIKE SUPERFAMILY
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / DNA replication / metal ion binding
Similarity search - Function
Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / MANGANESE (III) ION / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsShilova, A. / Lebrette, H. / Aurelius, O. / Hogbom, M. / Mueller, U.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2017-04018 Sweden
Knut and Alice Wallenberg FoundationWallenberg Academy Fellows 2017.0275 Sweden
European Research Council (ERC)HIGH-GEAR 724394 Sweden
CitationJournal: J.Synchrotron Radiat. / Year: 2020
Title: Current status and future opportunities for serial crystallography at MAX IV Laboratory.
Authors: Shilova, A. / Lebrette, H. / Aurelius, O. / Nan, J. / Welin, M. / Kovacic, R. / Ghosh, S. / Safari, C. / Friel, R.J. / Milas, M. / Matej, Z. / Hogbom, M. / Branden, G. / Kloos, M. / Shoeman, ...Authors: Shilova, A. / Lebrette, H. / Aurelius, O. / Nan, J. / Welin, M. / Kovacic, R. / Ghosh, S. / Safari, C. / Friel, R.J. / Milas, M. / Matej, Z. / Hogbom, M. / Branden, G. / Kloos, M. / Shoeman, R.L. / Doak, B. / Ursby, T. / Hakansson, M. / Logan, D.T. / Mueller, U.
History
DepositionFeb 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7203
Polymers39,6091
Non-polymers1112
Water41423
1
A: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4396
Polymers79,2182
Non-polymers2224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_335-y-2,-x-2,-z+1/21
Unit cell
Length a, b, c (Å)64.320, 64.320, 153.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-514-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase subunit beta


Mass: 39608.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338) (bacteria)
Gene: nrdB, SACE_1282, A8924_1677 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A4F980, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mn
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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 Å3/Da / Density % sol: 38.49 % / Description: square bipyramid
Crystal growTemperature: 294 K / Method: batch mode / pH: 4.5
Details: 16% (w/v) polyethylene glycol 3350, 2% (v/v) tacsimate pH 4.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→59.3 Å / Num. obs: 13245 / % possible obs: 98.6 % / Redundancy: 516 % / Biso Wilson estimate: 81.8 Å2 / CC1/2: 0.99 / Net I/σ(I): 6.73
Reflection shellResolution: 2.4→2.58 Å / Num. unique obs: 2336 / CC1/2: 0.64
Serial crystallography sample deliveryDescription: Silicon nitride membranes / Method: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
MxCuBEdata collection
PHENIXphasing
CrystFEL0.7.0data scaling
Coot0.8.9.2model building
CrystFEL0.7.0data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: Unpublished

Resolution: 2.4→59.3 Å / SU ML: 0.206 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.9869
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.221 653 5 %
Rwork0.1734 12407 -
obs0.1757 13060 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.39 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2493 0 2 23 2518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00282582
X-RAY DIFFRACTIONf_angle_d0.49183505
X-RAY DIFFRACTIONf_chiral_restr0.0354370
X-RAY DIFFRACTIONf_plane_restr0.0029459
X-RAY DIFFRACTIONf_dihedral_angle_d23.4779952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.2591240.22962336X-RAY DIFFRACTION96.06
2.59-2.850.25421250.21392417X-RAY DIFFRACTION98.26
2.85-3.260.27591300.20062471X-RAY DIFFRACTION98.93
3.26-4.10.18751330.18342497X-RAY DIFFRACTION99.7
4.1-59.30.221410.15942686X-RAY DIFFRACTION99.89

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