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- PDB-6f6m: R2-like ligand-binding oxidase Y162F mutant with anaerobically re... -

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Basic information

Entry
Database: PDB / ID: 6f6m
TitleR2-like ligand-binding oxidase Y162F 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: 1.393 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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)74,74010
Polymers73,8942
Non-polymers8468
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-78 kcal/mol
Surface area20330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.300, 55.599, 69.970
Angle α, β, γ (deg.)90.00, 113.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#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.: 218 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 22.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.0, streak-seeded with crystals of wild-type protein
PH range: 7

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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: 1.39→50 Å / Num. obs: 108553 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.036 / Rrim(I) all: 0.042 / Net I/σ(I): 15.08
Reflection shellResolution: 1.39→1.48 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.986 / Mean I/σ(I) obs: 1.06 / Num. unique obs: 15299 / CC1/2: 0.568 / Rrim(I) all: 1.223 / % possible all: 83.7

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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: 1.393→43.522 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.81
RfactorNum. reflection% reflectionSelection details
Rfree0.1867 2013 1.86 %random selection
Rwork0.1494 ---
obs0.1501 108378 95.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.393→43.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4595 0 42 218 4855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134825
X-RAY DIFFRACTIONf_angle_d0.9846470
X-RAY DIFFRACTIONf_dihedral_angle_d16.9951796
X-RAY DIFFRACTIONf_chiral_restr0.069674
X-RAY DIFFRACTIONf_plane_restr0.006835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3932-1.4280.38371150.37095948X-RAY DIFFRACTION75
1.428-1.46660.3491420.29277219X-RAY DIFFRACTION92
1.4666-1.50980.32431410.25177596X-RAY DIFFRACTION96
1.5098-1.55850.26671440.227681X-RAY DIFFRACTION97
1.5585-1.61420.24231380.20027691X-RAY DIFFRACTION97
1.6142-1.67880.25451510.17217695X-RAY DIFFRACTION97
1.6788-1.75530.20531530.15197799X-RAY DIFFRACTION99
1.7553-1.84780.19731400.14067800X-RAY DIFFRACTION99
1.8478-1.96360.18691460.13497670X-RAY DIFFRACTION97
1.9636-2.11520.19711450.13667850X-RAY DIFFRACTION99
2.1152-2.3280.17441490.1327819X-RAY DIFFRACTION99
2.328-2.66490.15651440.13537796X-RAY DIFFRACTION98
2.6649-3.35730.20571570.15357877X-RAY DIFFRACTION99
3.3573-43.54330.15551480.13927924X-RAY DIFFRACTION97

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