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- PDB-4hr5: R2-like ligand-binding oxidase without metal cofactor -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4hr5
TitleR2-like ligand-binding oxidase without metal cofactor
ComponentsRibonuleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-like ligand-binding oxidase / heterodinuclear Mn/Fe cofactor / ribonucleotide reductase R2 subunit fold / metalloprotein / manganese / iron / fatty acid/long-chain hydrocarbon ligand
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: 2.291 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Direct observation of structurally encoded metal discrimination and ether bond formation in a heterodinuclear metalloprotein
Authors: Griese, J.J. / Roos, K. / Cox, N. / Shafaat, H.S. / Branca, R.M.M. / Lehtio, J. / Graslund, A. / Lubitz, W. / Siegbahn, P.E.M. / Hogbom, M.
History
DepositionOct 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Ribonuleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2192
Polymers36,9631
Non-polymers2561
Water41423
1
A: Ribonuleotide reductase small subunit
hetero molecules

A: Ribonuleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4384
Polymers73,9262
Non-polymers5132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4670 Å2
ΔGint-14 kcal/mol
Surface area21680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.757, 97.043, 127.640
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-508-

HOH

21A-512-

HOH

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Components

#1: Protein Ribonuleotide reductase small subunit / R2-like ligand-binding oxidase


Mass: 36962.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA246 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-PLM / PALMITIC ACID


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


Mass: 18.015 Da / Num. of mol.: 23 / 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: 48.26 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17.5%(w/v) PEG 1500, 0.1M HEPES-Na, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.96 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jan 25, 2012
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.29→30 Å / Num. all: 16220 / Num. obs: 16220 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14.6 % / Biso Wilson estimate: 54.307 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 25.87
Reflection shellResolution: 2.29→2.43 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.754 / Mean I/σ(I) obs: 4.13 / Num. unique all: 2540 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DNAdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.291→28.378 Å / SU ML: 0.22 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 810 5 %random
Rwork0.1776 ---
all0.1805 16215 --
obs0.1805 16215 99.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.4 Å2
Refinement stepCycle: LAST / Resolution: 2.291→28.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 18 23 2286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152324
X-RAY DIFFRACTIONf_angle_d1.4983135
X-RAY DIFFRACTIONf_dihedral_angle_d16.318870
X-RAY DIFFRACTIONf_chiral_restr0.079327
X-RAY DIFFRACTIONf_plane_restr0.007403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.2905-2.4340.29521300.23722504263499
2.434-2.62180.281330.19825172650100
2.6218-2.88540.24081330.191325412674100
2.8854-3.30240.25011360.184525582694100
3.3024-4.15860.24081360.169525842720100
4.1586-28.38070.21451420.165427012843100

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