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- PDB-5omk: R2-like ligand-binding oxidase with aerobically reconstituted met... -

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Basic information

Entry
Database: PDB / ID: 5omk
TitleR2-like ligand-binding oxidase with aerobically reconstituted metal cofactor before photoconversion
ComponentsRibonucleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / DIIRON COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN OXIDOREDUCTASE
Function / homology
Function and homology information


deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
R2-like ligand binding oxidase / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.704 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J. Am. Chem. Soc. / Year: 2018
Title: Driving Protein Conformational Changes with Light: Photoinduced Structural Rearrangement in a Heterobimetallic Oxidase.
Authors: Maugeri, P.T. / Griese, J.J. / Branca, R.M. / Miller, E.K. / Smith, Z.R. / Eirich, J. / Hogbom, M. / Shafaat, H.S.
History
DepositionJul 31, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation / Item: _citation.title / _citation.year
Revision 1.2Feb 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3314
Polymers36,9631
Non-polymers3683
Water1,820101
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6628
Polymers73,9262
Non-polymers7366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7560 Å2
ΔGint-78 kcal/mol
Surface area20450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.666, 96.624, 128.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-523-

HOH

21A-553-

HOH

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Components

#1: Protein Ribonucleotide reductase small subunit


Mass: 36962.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.34 Å3/Da / Density % sol: 47.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3 / Details: 25% (w/v) PEG 1500, 0.1 M HEPES-Na pH 7.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 38162 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 34.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 6.3 % / Rmerge(I) obs: 3.077 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 6063 / CC1/2: 0.121 / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HR0

4hr0


Resolution: 1.704→48.312 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.46
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1908 5 %random selection
Rwork0.1781 ---
obs0.1796 38157 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.704→48.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 20 101 2478
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132451
X-RAY DIFFRACTIONf_angle_d1.0753296
X-RAY DIFFRACTIONf_dihedral_angle_d18.3731450
X-RAY DIFFRACTIONf_chiral_restr0.055344
X-RAY DIFFRACTIONf_plane_restr0.007425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7044-1.74710.35711320.38622501X-RAY DIFFRACTION98
1.7471-1.79430.37291350.36422572X-RAY DIFFRACTION100
1.7943-1.84710.35661350.34362564X-RAY DIFFRACTION100
1.8471-1.90670.33791300.31782537X-RAY DIFFRACTION100
1.9067-1.97490.32041420.2892587X-RAY DIFFRACTION100
1.9749-2.05390.30031320.24382546X-RAY DIFFRACTION100
2.0539-2.14740.23781350.20922597X-RAY DIFFRACTION100
2.1474-2.26060.25091360.19192548X-RAY DIFFRACTION100
2.2606-2.40230.18221360.16572590X-RAY DIFFRACTION100
2.4023-2.58770.20371370.15642596X-RAY DIFFRACTION100
2.5877-2.84810.20051370.16232597X-RAY DIFFRACTION100
2.8481-3.26020.20111380.16622626X-RAY DIFFRACTION100
3.2602-4.10710.18011380.15082634X-RAY DIFFRACTION100
4.1071-48.33140.17991450.1542754X-RAY DIFFRACTION100

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