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- PDB-6f65: R2-like ligand-binding oxidase A171F mutant with aerobically reco... -

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Basic information

Entry
Database: PDB / ID: 6f65
TitleR2-like ligand-binding oxidase A171F 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, 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
: / : / MANGANESE (III) ION / OCTANOIC ACID (CAPRYLIC ACID) / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.948 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 1.1Jan 23, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.2Feb 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 1.3Mar 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Jan 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.pdbx_ptnr1_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3495
Polymers37,0391
Non-polymers3104
Water1,08160
1
A: Ribonucleotide reductase small subunit
hetero molecules

A: Ribonucleotide reductase small subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,69810
Polymers74,0782
Non-polymers6208
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area7090 Å2
ΔGint-57 kcal/mol
Surface area21090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.966, 97.196, 128.233
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-518-

HOH

21A-533-

HOH

31A-539-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribonucleotide reductase small subunit


Mass: 37038.902 Da / Num. of mol.: 1 / Mutation: A171F
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, 64 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
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 PILATUS 6M-F / Detector: PIXEL / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.948→50 Å / Num. obs: 25690 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 43.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.045 / Rrim(I) all: 0.052 / Net I/σ(I): 15.33
Reflection shellResolution: 1.948→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.877 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 4075 / CC1/2: 0.604 / Rrim(I) all: 1.034 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4HR0

4hr0


Resolution: 1.948→48.5 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2071 1285 5 %random selection
Rwork0.1772 ---
obs0.1787 25686 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.948→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 13 60 2436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182459
X-RAY DIFFRACTIONf_angle_d1.0943303
X-RAY DIFFRACTIONf_dihedral_angle_d16.2281444
X-RAY DIFFRACTIONf_chiral_restr0.059344
X-RAY DIFFRACTIONf_plane_restr0.008427
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.948-2.0260.37721390.36162635X-RAY DIFFRACTION98
2.026-2.11820.30351420.26472702X-RAY DIFFRACTION100
2.1182-2.22990.25191430.22462707X-RAY DIFFRACTION100
2.2299-2.36960.23891420.19352705X-RAY DIFFRACTION100
2.3696-2.55260.21011420.17712706X-RAY DIFFRACTION100
2.5526-2.80940.20081430.18272704X-RAY DIFFRACTION99
2.8094-3.21590.22581430.18472737X-RAY DIFFRACTION99
3.2159-4.05140.2091430.16652714X-RAY DIFFRACTION98
4.0514-48.51540.17371480.15442791X-RAY DIFFRACTION97

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