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- PDB-6f6l: R2-like ligand-binding oxidase Y162F mutant with aerobically reco... -

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Basic information

Entry
Database: PDB / ID: 6f6l
TitleR2-like ligand-binding oxidase Y162F 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 / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2019
Title: Assembly of a heterodinuclear Mn/Fe cofactor is coupled to tyrosine-valine ether cross-link formation in the R2-like ligand-binding oxidase.
Authors: Griese, J.J. / Kositzki, R. / Haumann, M. / Hogbom, M.
History
DepositionDec 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 19, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 17, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)74,73810
Polymers73,8942
Non-polymers8448
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-69 kcal/mol
Surface area20390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.748, 55.730, 69.456
Angle α, β, γ (deg.)90.00, 113.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ribonucleotide reductase small subunit


Mass: 36946.809 Da / Num. of mol.: 2 / Mutation: Y162F
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, 119 molecules

#2: Chemical ChemComp-MN3 / MANGANESE (III) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2
#6: 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: 1.95 Å3/Da / Density % sol: 36.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 22.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 6.9, streak-seeded with crystals of wild-type protein
PH range: 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 42300 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 39 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.051 / Net I/σ(I): 14.87
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 1.59 / Num. unique obs: 5645 / CC1/2: 0.676 / Rrim(I) all: 0.828 / % possible all: 78.6

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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: 4HR0

4hr0


Resolution: 1.904→43.463 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.11
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 2117 5.01 %random selection
Rwork0.1657 ---
obs0.1676 42235 94.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.904→43.463 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 0 42 111 4748
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0174783
X-RAY DIFFRACTIONf_angle_d1.0526417
X-RAY DIFFRACTIONf_dihedral_angle_d14.5692823
X-RAY DIFFRACTIONf_chiral_restr0.053669
X-RAY DIFFRACTIONf_plane_restr0.007826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9035-1.94780.4643820.44221449X-RAY DIFFRACTION52
1.9478-1.99650.34591410.29922714X-RAY DIFFRACTION95
1.9965-2.05050.30791430.25912738X-RAY DIFFRACTION98
2.0505-2.11080.30761450.2492745X-RAY DIFFRACTION98
2.1108-2.17890.27631440.21762776X-RAY DIFFRACTION98
2.1789-2.25680.2671410.19882729X-RAY DIFFRACTION97
2.2568-2.34720.23861460.17842768X-RAY DIFFRACTION98
2.3472-2.4540.23781410.17112759X-RAY DIFFRACTION97
2.454-2.58340.20911450.16672682X-RAY DIFFRACTION95
2.5834-2.74520.20651480.17092792X-RAY DIFFRACTION98
2.7452-2.95710.2311460.17012799X-RAY DIFFRACTION98
2.9571-3.25460.21571490.18022785X-RAY DIFFRACTION98
3.2546-3.72530.19071450.15642729X-RAY DIFFRACTION95
3.7253-4.69260.16321510.12772819X-RAY DIFFRACTION98
4.6926-43.4740.16911500.14792834X-RAY DIFFRACTION96

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