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- PDB-6qk0: R2-like ligand-binding oxidase E69D mutant with anaerobically rec... -

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Basic information

Entry
Database: PDB / ID: 6qk0
TitleR2-like ligand-binding oxidase E69D 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
: / : / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.091 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Key Structural Motifs Balance Metal Binding and Oxidative Reactivity in a Heterobimetallic Mn/Fe Protein.
Authors: Kisgeropoulos, E.C. / Griese, J.J. / Smith, Z.R. / Branca, R.M.M. / Schneider, C.R. / Hogbom, M. / Shafaat, H.S.
History
DepositionJan 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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
Revision 1.2Jan 24, 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: Ribonucleotide reductase small subunit
B: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,74410
Polymers73,8982
Non-polymers8468
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-71 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.808, 55.963, 98.059
Angle α, β, γ (deg.)90.00, 126.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonucleotide reductase small subunit


Mass: 36948.781 Da / Num. of mol.: 2 / Mutation: E69D
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.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.41 Å3/Da / Density % sol: 48.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 30% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.7

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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: 2.09→50 Å / Num. obs: 40539 / % possible obs: 96.3 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 39.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.079 / Net I/σ(I): 13
Reflection shellResolution: 2.09→2.22 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.799 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 6205 / CC1/2: 0.723 / Rrim(I) all: 0.945 / % possible all: 91.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR4

4hr4


Resolution: 2.091→48.601 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.92
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 2026 5 %random
Rwork0.2093 ---
obs0.212 40492 96.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.091→48.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4529 0 42 82 4653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0214695
X-RAY DIFFRACTIONf_angle_d1.2626301
X-RAY DIFFRACTIONf_dihedral_angle_d13.0732778
X-RAY DIFFRACTIONf_chiral_restr0.065659
X-RAY DIFFRACTIONf_plane_restr0.009808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0909-2.14320.40211270.37592412X-RAY DIFFRACTION85
2.1432-2.20110.32931440.32082726X-RAY DIFFRACTION97
2.2011-2.26590.52291390.432630X-RAY DIFFRACTION93
2.2659-2.3390.36191460.2922771X-RAY DIFFRACTION97
2.339-2.42260.33041470.25512792X-RAY DIFFRACTION99
2.4226-2.51960.30781470.24112795X-RAY DIFFRACTION99
2.5196-2.63430.30281460.22912770X-RAY DIFFRACTION99
2.6343-2.77310.27241460.24342775X-RAY DIFFRACTION98
2.7731-2.94690.29471490.22692819X-RAY DIFFRACTION99
2.9469-3.17430.32311470.22772798X-RAY DIFFRACTION99
3.1743-3.49370.22981470.2022801X-RAY DIFFRACTION98
3.4937-3.99910.23651450.18482759X-RAY DIFFRACTION97
3.9991-5.03760.20881460.15422777X-RAY DIFFRACTION97
5.0376-48.61450.21721500.17642841X-RAY DIFFRACTION96

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