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- PDB-6f6g: R2-like ligand-binding oxidase V72I mutant with anaerobically rec... -

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Basic information

Entry
Database: PDB / ID: 6f6g
TitleR2-like ligand-binding oxidase V72I 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
: / : / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 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.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)74,80010
Polymers73,9542
Non-polymers8468
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-74 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.988, 98.467, 55.862
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonucleotide reductase small subunit


Mass: 36976.832 Da / Num. of mol.: 2 / 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
#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-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.: 136 / 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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 30% (W/V) PEG 1500, 0.1 M HEPES-NA PH 7.5 / PH range: 7.5

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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: 1.99→50 Å / Num. obs: 48652 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 39.2 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.137 / Rrim(I) all: 0.149 / Net I/σ(I): 9.67
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.828 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 7415 / CC1/2: 0.329 / Rrim(I) all: 1.999 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HR4

4hr4


Resolution: 1.991→48.588 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.98
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 2432 5 %random selection
Rwork0.1927 ---
obs0.1951 48623 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.991→48.588 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4617 0 42 136 4795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0194850
X-RAY DIFFRACTIONf_angle_d1.2096507
X-RAY DIFFRACTIONf_dihedral_angle_d17.432855
X-RAY DIFFRACTIONf_chiral_restr0.059676
X-RAY DIFFRACTIONf_plane_restr0.008839
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9914-2.03210.39461220.34752312X-RAY DIFFRACTION86
2.0321-2.07630.35981430.31722714X-RAY DIFFRACTION100
2.0763-2.12460.36591410.28552683X-RAY DIFFRACTION100
2.1246-2.17770.29981440.25742733X-RAY DIFFRACTION100
2.1777-2.23660.30371430.25382722X-RAY DIFFRACTION100
2.2366-2.30240.3341410.25132684X-RAY DIFFRACTION100
2.3024-2.37670.25091430.23352720X-RAY DIFFRACTION100
2.3767-2.46160.30571440.22972720X-RAY DIFFRACTION100
2.4616-2.56020.32651410.24152681X-RAY DIFFRACTION98
2.5602-2.67670.33911420.25572711X-RAY DIFFRACTION100
2.6767-2.81780.26411450.19922746X-RAY DIFFRACTION100
2.8178-2.99430.28271440.18712729X-RAY DIFFRACTION100
2.9943-3.22550.24051450.1992759X-RAY DIFFRACTION100
3.2255-3.550.21511450.17362762X-RAY DIFFRACTION100
3.55-4.06350.19411470.15222781X-RAY DIFFRACTION100
4.0635-5.11860.18281470.1422806X-RAY DIFFRACTION100
5.1186-48.60210.19251550.17772928X-RAY DIFFRACTION99

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