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- PDB-6qjv: R2-like ligand-binding oxidase E69D mutant with aerobically recon... -

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Basic information

Entry
Database: PDB / ID: 6qjv
TitleR2-like ligand-binding oxidase E69D mutant with aerobically 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, 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
: / : / MANGANESE (III) ION / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.905 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 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 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_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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3715
Polymers36,9491
Non-polymers4224
Water2,018112
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,74210
Polymers73,8982
Non-polymers8448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7740 Å2
ΔGint-68 kcal/mol
Surface area21070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.870, 96.824, 129.200
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-525-

HOH

21A-573-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribonucleotide reductase small subunit


Mass: 36948.781 Da / Num. of mol.: 1 / 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

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Non-polymers , 5 types, 116 molecules

#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 30% (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: 0.9999 Å
DetectorType: DECTRIS PILATUS 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: 1.9→50 Å / Num. obs: 27535 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 30.62 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.06 / Net I/σ(I): 14.49
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.658 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 4310 / CC1/2: 0.691 / Rrim(I) all: 0.79 / % possible all: 97.1

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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: 1.905→39.35 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.89
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1369 4.98 %random selection
Rwork0.1636 ---
obs0.1657 27517 98.78 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.905→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2356 0 21 112 2489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162454
X-RAY DIFFRACTIONf_angle_d1.0233295
X-RAY DIFFRACTIONf_dihedral_angle_d15.8131451
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 (%)
1.9046-1.97270.29381290.28682506X-RAY DIFFRACTION96
1.9727-2.05160.30051300.23192559X-RAY DIFFRACTION99
2.0516-2.1450.2511390.21162579X-RAY DIFFRACTION99
2.145-2.25810.24331350.18822590X-RAY DIFFRACTION99
2.2581-2.39950.19651380.16722613X-RAY DIFFRACTION100
2.3995-2.58480.20561390.15222632X-RAY DIFFRACTION99
2.5848-2.84480.22451360.15872616X-RAY DIFFRACTION99
2.8448-3.25630.1891380.16232630X-RAY DIFFRACTION99
3.2563-4.10190.17531380.14452655X-RAY DIFFRACTION99
4.1019-39.35810.19191470.14862768X-RAY DIFFRACTION99

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