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- PDB-6i95: R2-like ligand-binding oxidase G68L mutant with anaerobically rec... -

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Basic information

Entry
Database: PDB / ID: 6i95
TitleR2-like ligand-binding oxidase G68L mutant with anaerobically reconstituted Mn/Fe cofactor
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 small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / 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: 1.646 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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)37,3305
Polymers37,0191
Non-polymers3114
Water1,838102
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,65910
Polymers74,0382
Non-polymers6228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area6930 Å2
ΔGint-42 kcal/mol
Surface area20750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.958, 97.602, 127.528
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-548-

HOH

21A-562-

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.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


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


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 27.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.646→50 Å / Num. obs: 41902 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 32.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rrim(I) all: 0.042 / Net I/σ(I): 23.09
Reflection shellResolution: 1.646→1.75 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 2 / Num. unique obs: 6490 / CC1/2: 0.75 / Rrim(I) all: 1.018 / % possible all: 95.2

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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: 4HR4

4hr4


Resolution: 1.646→48.801 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.06
RfactorNum. reflection% reflectionSelection details
Rfree0.2037 2086 4.98 %random selection
Rwork0.1734 ---
obs0.1749 41896 98.1 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.646→48.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2278 0 13 102 2393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132406
X-RAY DIFFRACTIONf_angle_d1.1013236
X-RAY DIFFRACTIONf_dihedral_angle_d13.1361421
X-RAY DIFFRACTIONf_chiral_restr0.055337
X-RAY DIFFRACTIONf_plane_restr0.007418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6463-1.68460.35821290.32072456X-RAY DIFFRACTION92
1.6846-1.72680.27861370.26832602X-RAY DIFFRACTION98
1.7268-1.77340.26761360.23712591X-RAY DIFFRACTION97
1.7734-1.82560.25441380.22192615X-RAY DIFFRACTION98
1.8256-1.88460.26551380.21392641X-RAY DIFFRACTION98
1.8846-1.95190.24491320.20432620X-RAY DIFFRACTION98
1.9519-2.03010.23161360.19432641X-RAY DIFFRACTION99
2.0301-2.12250.23481410.18432684X-RAY DIFFRACTION99
2.1225-2.23440.21380.17432659X-RAY DIFFRACTION99
2.2344-2.37440.20021410.1622657X-RAY DIFFRACTION99
2.3744-2.55770.20861390.1612683X-RAY DIFFRACTION99
2.5577-2.8150.20951450.16892695X-RAY DIFFRACTION99
2.815-3.22230.20661430.17622697X-RAY DIFFRACTION99
3.2223-4.05950.17711430.16022749X-RAY DIFFRACTION99
4.0595-48.82240.19371500.16512820X-RAY DIFFRACTION98

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