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- PDB-6f6f: R2-like ligand-binding oxidase V72I mutant with aerobically recon... -

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Basic information

Entry
Database: PDB / ID: 6f6f
TitleR2-like ligand-binding oxidase V72I 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 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
: / : / MANGANESE (III) ION / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.788 Å
AuthorsGriese, J.J. / Hogbom, M.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: Ether cross-link formation in the R2-like ligand-binding oxidase.
Authors: Griese, J.J. / Branca, R.M.M. / Srinivas, V. / Hogbom, M.
History
DepositionDec 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 1, 2018Group: Data collection / 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 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_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)37,3995
Polymers36,9771
Non-polymers4224
Water1,00956
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,79810
Polymers73,9542
Non-polymers8448
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7370 Å2
ΔGint-65 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.583, 95.899, 127.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-533-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribonucleotide reductase small subunit


Mass: 36976.832 Da / Num. of mol.: 1 / Mutation: V72I
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, 60 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.: 56 / 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: 2.57 Å3/Da / Density % sol: 52.11 %
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 / PH range: 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.788→50 Å / Num. obs: 32199 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 41.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.079 / Net I/σ(I): 13.29
Reflection shellResolution: 1.788→1.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 2.121 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 9412 / CC1/2: 0.158 / Rrim(I) all: 2.292 / % possible all: 94.7

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Processing

Software
NameVersionClassification
XDSdata reduction
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HR0

4hr0


Resolution: 1.788→48.089 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.4
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1605 4.99 %random selection
Rwork0.1749 ---
obs0.1765 32148 98.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 144.26 Å2 / Biso mean: 53.9731 Å2 / Biso min: 27.38 Å2
Refinement stepCycle: final / Resolution: 1.788→48.089 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2341 0 52 56 2449
Biso mean--58.7 47.32 -
Num. residues----283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152426
X-RAY DIFFRACTIONf_angle_d1.1163259
X-RAY DIFFRACTIONf_chiral_restr0.069340
X-RAY DIFFRACTIONf_plane_restr0.007420
X-RAY DIFFRACTIONf_dihedral_angle_d18.0481435
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7879-1.84560.37941330.35922521265491
1.8456-1.91160.31541460.30962770291699
1.9116-1.98810.2871440.276627872931100
1.9881-2.07860.24941470.23772771291899
2.0786-2.18820.2731470.211327902937100
2.1882-2.32520.21891480.19332792294099
2.3252-2.50480.19671480.16942798294699
2.5048-2.75680.19521490.16382741289097
2.7568-3.15570.18491440.17082819296399
3.1557-3.97550.18671520.16352852300499
3.9755-48.10680.20111470.15642902304997

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