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- PDB-6i94: R2-like ligand-binding oxidase G68L mutant with non-activated Mn/... -

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Basic information

Entry
Database: PDB / ID: 6i94
TitleR2-like ligand-binding oxidase G68L mutant with non-activated Mn/Mn cofactor (after aerobic reconstitution with Mn and Fe)
ComponentsRibonucleotide reductase small subunit
KeywordsOXIDOREDUCTASE / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE 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
: / OCTANOIC ACID (CAPRYLIC ACID) / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.703 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins.
Authors: Kutin, Y. / Kositzki, R. / Branca, R.M.M. / Srinivas, V. / Lundin, D. / Haumann, M. / Hogbom, M. / Cox, N. / Griese, J.J.
History
DepositionNov 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3285
Polymers37,0191
Non-polymers3094
Water2,000111
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,65610
Polymers74,0382
Non-polymers6188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6890 Å2
ΔGint-33 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.815, 97.200, 126.921
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-565-

HOH

21A-579-

HOH

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Components

#1: Protein Ribonucleotide reductase small subunit


Mass: 37018.910 Da / Num. of mol.: 1 / Mutation: G68L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: GK2771 / Plasmid: pET-46 Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q5KW80, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.33 Å3/Da / Density % sol: 47.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 27.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 37827 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.034 / Rrim(I) all: 0.04 / Net I/σ(I): 18.05
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 1.71 / Num. unique obs: 5904 / CC1/2: 0.709 / Rrim(I) all: 0.684

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HR0

4hr0


Resolution: 1.703→38.792 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 19.78
RfactorNum. reflection% reflectionSelection details
Rfree0.2005 1891 5 %random selection
Rwork0.174 ---
obs0.1753 37816 98.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.703→38.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2269 0 13 111 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122398
X-RAY DIFFRACTIONf_angle_d1.0423228
X-RAY DIFFRACTIONf_dihedral_angle_d15.9461417
X-RAY DIFFRACTIONf_chiral_restr0.054336
X-RAY DIFFRACTIONf_plane_restr0.006417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7027-1.74530.33261260.29672399X-RAY DIFFRACTION94
1.7453-1.79240.28981310.24622511X-RAY DIFFRACTION98
1.7924-1.84520.23691350.21562550X-RAY DIFFRACTION100
1.8452-1.90470.24781350.20572546X-RAY DIFFRACTION100
1.9047-1.97280.24541340.1922562X-RAY DIFFRACTION99
1.9728-2.05180.21731330.18772543X-RAY DIFFRACTION100
2.0518-2.14520.21231340.17622565X-RAY DIFFRACTION99
2.1452-2.25830.19641350.16472539X-RAY DIFFRACTION99
2.2583-2.39970.1951360.15872578X-RAY DIFFRACTION100
2.3997-2.5850.18071360.15872571X-RAY DIFFRACTION99
2.585-2.84510.18561360.16492592X-RAY DIFFRACTION100
2.8451-3.25660.19031390.17562623X-RAY DIFFRACTION100
3.2566-4.10220.1851360.16622609X-RAY DIFFRACTION99
4.1022-38.80180.20111450.16922737X-RAY DIFFRACTION99

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