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- PDB-6f6k: R2-like ligand-binding oxidase V72L mutant with anaerobically rec... -

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Basic information

Entry
Database: PDB / ID: 6f6k
TitleR2-like ligand-binding oxidase V72L 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, 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
LAURIC ACID / : / : / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.982 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 / 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.pdbx_ptnr1_label_alt_id / _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

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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)74,68810
Polymers73,9542
Non-polymers7348
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6990 Å2
ΔGint-48 kcal/mol
Surface area20520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.612, 55.655, 70.075
Angle α, β, γ (deg.)90.00, 114.16, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ribonucleotide reductase small subunit


Mass: 36976.832 Da / Num. of mol.: 2 / Mutation: V72L
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-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 22.5% (W/V) PEG 1500, 0.1 M HEPES-NA PH 6.8, streak-seeded with crystals of wild-type protein
PH range: 6.8

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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: 1.98→50 Å / Num. obs: 37786 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.16 / Net I/σ(I): 6.37
Reflection shellResolution: 1.98→2.1 Å / Redundancy: 3.2 % / Rmerge(I) obs: 1.142 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 5524 / CC1/2: 0.443 / Rrim(I) all: 1.365 / % possible all: 88

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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: 1.982→43.574 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.42
RfactorNum. reflection% reflectionSelection details
Rfree0.2632 1888 5 %random selection
Rwork0.1979 ---
obs0.2011 37747 95.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.982→43.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 34 161 4702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164702
X-RAY DIFFRACTIONf_angle_d1.2066308
X-RAY DIFFRACTIONf_dihedral_angle_d15.0832774
X-RAY DIFFRACTIONf_chiral_restr0.056657
X-RAY DIFFRACTIONf_plane_restr0.007812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9816-2.03520.44011250.35872187X-RAY DIFFRACTION78
2.0352-2.09510.37811430.33312776X-RAY DIFFRACTION97
2.0951-2.16270.3521520.2942793X-RAY DIFFRACTION97
2.1627-2.240.34931380.27212797X-RAY DIFFRACTION97
2.24-2.32970.29741490.2532725X-RAY DIFFRACTION96
2.3297-2.43570.28371460.2362788X-RAY DIFFRACTION96
2.4357-2.56410.33321470.22482765X-RAY DIFFRACTION96
2.5641-2.72470.23061470.20022818X-RAY DIFFRACTION98
2.7247-2.93510.32781470.20162862X-RAY DIFFRACTION99
2.9351-3.23040.28051480.19982840X-RAY DIFFRACTION98
3.2304-3.69760.23911490.17282737X-RAY DIFFRACTION94
3.6976-4.65770.19071440.14792859X-RAY DIFFRACTION98
4.6577-43.5850.22651530.17242912X-RAY DIFFRACTION97

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