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- PDB-6qo5: Crystal structure of apo (metal-free) ribonucleotide reductase Nr... -

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Basic information

Entry
Database: PDB / ID: 6qo5
TitleCrystal structure of apo (metal-free) ribonucleotide reductase NrdF from Bacillus anthracis
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsOXIDOREDUCTASE / Metal binding / Oxidation reduction process / 2'-Deoxyribonucleotide metabolism / DNA replication
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding / membrane
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily ...Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.511 Å
AuthorsGrave, K. / Hogbom, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2019
Title: Redox-induced structural changes in the di-iron and di-manganese forms of Bacillus anthracis ribonucleotide reductase subunit NrdF suggest a mechanism for gating of radical access.
Authors: Grave, K. / Lambert, W. / Berggren, G. / Griese, J.J. / Bennett, M.D. / Logan, D.T. / Hogbom, M.
History
DepositionFeb 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 2, 2019Group: 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 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2434
Polymers74,1122
Non-polymers1322
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-57 kcal/mol
Surface area21650 Å2
Unit cell
Length a, b, c (Å)57.185, 59.806, 95.234
Angle α, β, γ (deg.)90.00, 107.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ribonucleoside-diphosphate reductase subunit beta


Mass: 37055.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: nrdF, GBAA_1372 / Variant: pXO1-/pXO2- deficient / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2
References: UniProt: Q81TB4, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8 - 2.0 M ammonium sulphate, 0.1 M Bis-Tris methane pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.51→40.35 Å / Num. obs: 95759 / % possible obs: 99.46 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.0261 / Rrim(I) all: 0.051 / Net I/σ(I): 16.35
Reflection shellResolution: 1.51→1.57 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.622 / Mean I/σ(I) obs: 2.11 / Num. unique obs: 9403 / CC1/2: 0.805 / Rpim(I) all: 0.365 / Rrim(I) all: 0.723 / % possible all: 97.94

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KGN

1kgn


Resolution: 1.511→40.35 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.69
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 4788 5 %Random selection
Rwork0.1651 ---
obs0.1665 95759 99.46 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.511→40.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4722 0 6 302 5030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114883
X-RAY DIFFRACTIONf_angle_d1.0926611
X-RAY DIFFRACTIONf_dihedral_angle_d14.292917
X-RAY DIFFRACTIONf_chiral_restr0.06733
X-RAY DIFFRACTIONf_plane_restr0.007843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5112-1.52840.29481500.27792862X-RAY DIFFRACTION94
1.5284-1.54640.30751600.26643031X-RAY DIFFRACTION100
1.5464-1.56520.29791600.25873040X-RAY DIFFRACTION100
1.5652-1.5850.31311590.24523016X-RAY DIFFRACTION100
1.585-1.60590.30851570.22832997X-RAY DIFFRACTION100
1.6059-1.62790.25681610.22413046X-RAY DIFFRACTION100
1.6279-1.65120.27391600.21973038X-RAY DIFFRACTION100
1.6512-1.67580.25841590.21853034X-RAY DIFFRACTION100
1.6758-1.7020.23061590.21173015X-RAY DIFFRACTION100
1.702-1.72990.23621600.19973034X-RAY DIFFRACTION100
1.7299-1.75970.23191600.19443047X-RAY DIFFRACTION100
1.7597-1.79170.26231590.18943025X-RAY DIFFRACTION100
1.7917-1.82620.23761570.18842982X-RAY DIFFRACTION100
1.8262-1.86350.21941610.17953058X-RAY DIFFRACTION100
1.8635-1.9040.23761590.17813026X-RAY DIFFRACTION100
1.904-1.94830.2231590.18183008X-RAY DIFFRACTION100
1.9483-1.9970.19431600.16663049X-RAY DIFFRACTION100
1.997-2.0510.19521610.16043045X-RAY DIFFRACTION100
2.051-2.11130.18111600.15883041X-RAY DIFFRACTION100
2.1113-2.17950.19461590.14993028X-RAY DIFFRACTION100
2.1795-2.25740.16881580.14323009X-RAY DIFFRACTION100
2.2574-2.34770.18721610.1433061X-RAY DIFFRACTION100
2.3477-2.45460.1831610.14913050X-RAY DIFFRACTION100
2.4546-2.5840.17031600.14463048X-RAY DIFFRACTION100
2.584-2.74580.16821610.1493045X-RAY DIFFRACTION100
2.7458-2.95780.16231600.16513037X-RAY DIFFRACTION99
2.9578-3.25540.17881590.16723035X-RAY DIFFRACTION99
3.2554-3.72620.16811620.14173079X-RAY DIFFRACTION100
3.7262-4.69350.15021620.12793066X-RAY DIFFRACTION99
4.6935-41.77990.20651640.18483119X-RAY DIFFRACTION98

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