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- PDB-6f6c: R2-like ligand-binding oxidase V72A mutant with aerobically recon... -

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Basic information

Entry
Database: PDB / ID: 6f6c
TitleR2-like ligand-binding oxidase V72A 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 / MOLECULAR REPLACEMENT / Resolution: 1.766 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)74,71410
Polymers73,8702
Non-polymers8448
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint-68 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.462, 55.818, 69.741
Angle α, β, γ (deg.)90.00, 114.09, 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: 36934.754 Da / Num. of mol.: 2 / Mutation: V72A
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, 160 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-MN3 / MANGANESE (III) 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.: 152 / 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: 37.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 20% (W/V) PEG 1500, 0.1 M HEPES-NA PH 6.9, streak-seeded with crystals of the 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: 1.766→50 Å / Num. obs: 53633 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 33.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.054 / Net I/σ(I): 13.7
Reflection shellResolution: 1.766→1.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 7702 / CC1/2: 0.725 / Rrim(I) all: 0.936 / % possible all: 85.1

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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: 1.766→43.574 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2674 4.99 %random selection
Rwork0.1795 ---
obs0.1817 53596 95.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.766→43.574 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4593 0 42 152 4787
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0164784
X-RAY DIFFRACTIONf_angle_d1.0416415
X-RAY DIFFRACTIONf_dihedral_angle_d14.1172823
X-RAY DIFFRACTIONf_chiral_restr0.055667
X-RAY DIFFRACTIONf_plane_restr0.007826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7659-1.7980.4806890.47571624X-RAY DIFFRACTION58
1.798-1.83260.36651420.30732738X-RAY DIFFRACTION98
1.8326-1.870.30061440.27982749X-RAY DIFFRACTION98
1.87-1.91060.27091450.27162706X-RAY DIFFRACTION97
1.9106-1.95510.32811390.26692626X-RAY DIFFRACTION95
1.9551-2.0040.27861430.23382736X-RAY DIFFRACTION98
2.004-2.05810.27691440.21812769X-RAY DIFFRACTION99
2.0581-2.11870.29051460.21182741X-RAY DIFFRACTION98
2.1187-2.18710.24471430.2042759X-RAY DIFFRACTION99
2.1871-2.26530.22461450.18832756X-RAY DIFFRACTION98
2.2653-2.35590.23121440.18012744X-RAY DIFFRACTION98
2.3559-2.46320.25551420.18192704X-RAY DIFFRACTION97
2.4632-2.5930.24591450.17832696X-RAY DIFFRACTION96
2.593-2.75540.24241450.17722753X-RAY DIFFRACTION98
2.7554-2.96820.20121430.17972763X-RAY DIFFRACTION98
2.9682-3.26680.22411440.18722748X-RAY DIFFRACTION97
3.2668-3.73920.23271370.17372679X-RAY DIFFRACTION94
3.7392-4.71020.17961490.13932803X-RAY DIFFRACTION98
4.7102-43.58750.18641450.16252828X-RAY DIFFRACTION97

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