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- PDB-6qo9: Crystal structure of ribonucleotide reductase NrdF from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 6qo9
TitleCrystal structure of ribonucleotide reductase NrdF from Bacillus anthracis soaked with manganese ions
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: 1.299 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 ...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_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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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)75,23113
Polymers74,1122
Non-polymers1,11911
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-92 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.529, 61.231, 95.836
Angle α, β, γ (deg.)90.000, 106.478, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
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: 1.299→28.7602449565 Å / Num. obs: 155351 / % possible obs: 99 % / Redundancy: 3.3 % / Biso Wilson estimate: 10.749 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.031 / Rrim(I) all: 0.057 / Net I/σ(I): 14.9
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 15233 / CC1/2: 0.796 / Rpim(I) all: 0.338 / Rrim(I) all: 0.632 / % possible all: 97.65

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.12_2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QO5

6qo5


Resolution: 1.299→28.76 Å / SU ML: 0.0956969656831 / Cross valid method: FREE R-VALUE / σ(F): 1.353 / Phase error: 14.7212112245
RfactorNum. reflection% reflectionSelection details
Rfree0.159 7756 4.998 %Random selection
Rwork0.136 ---
obs0.137 155158 98.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.981 Å2
Refinement stepCycle: LAST / Resolution: 1.299→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4670 0 57 492 5219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01202048944114999
X-RAY DIFFRACTIONf_angle_d1.208591766646790
X-RAY DIFFRACTIONf_chiral_restr0.0811594580925745
X-RAY DIFFRACTIONf_plane_restr0.00759049329326865
X-RAY DIFFRACTIONf_dihedral_angle_d20.88229988391864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2999-1.31470.229211568312430.2091425948124619X-RAY DIFFRACTION92.6801372474
1.3147-1.33010.2056613999322570.1873791603714891X-RAY DIFFRACTION99.1143627262
1.3301-1.34640.2076842109542570.1863560963544884X-RAY DIFFRACTION99.3238021638
1.3464-1.36340.219637244842580.1882914549684889X-RAY DIFFRACTION98.7907869482
1.3634-1.38130.2076848832532500.186825174954751X-RAY DIFFRACTION96.3398189174
1.3813-1.40030.2026432557542600.167166124914930X-RAY DIFFRACTION99.0836197022
1.4003-1.42030.1788308886442580.1523534382834911X-RAY DIFFRACTION99.7298861663
1.4203-1.44150.1653270042922580.1523977496894897X-RAY DIFFRACTION99.5750434615
1.4415-1.4640.1930428253842570.1520258076584877X-RAY DIFFRACTION98.579109063
1.464-1.4880.1951963697662560.1394722461844876X-RAY DIFFRACTION98.6354026523
1.488-1.51360.1555561118622610.1281242388344945X-RAY DIFFRACTION99.1619047619
1.5136-1.54120.1707287727482530.1270974213254812X-RAY DIFFRACTION98.1208833785
1.5412-1.57080.1495318015732610.1122441623954963X-RAY DIFFRACTION99.6946564885
1.5708-1.60290.1440027136452610.1069520603544957X-RAY DIFFRACTION99.9616858238
1.6029-1.63770.1515417362072600.1051958311594923X-RAY DIFFRACTION99.8651252408
1.6377-1.67580.1413452249912600.1104687499494949X-RAY DIFFRACTION99.980806142
1.6758-1.71770.1556870122132610.1119172806214956X-RAY DIFFRACTION99.7514340344
1.7177-1.76420.1378740981072590.1079974641924926X-RAY DIFFRACTION99.5010554596
1.7642-1.81610.1483970666392600.1067950788164937X-RAY DIFFRACTION99.846301633
1.8161-1.87470.1177877549742600.1081265067134941X-RAY DIFFRACTION99.6933103316
1.8747-1.94170.1528819730952560.1194641134794866X-RAY DIFFRACTION97.9724560061
1.9417-2.01940.1540452522752590.1200913763624937X-RAY DIFFRACTION99.2360580596
2.0194-2.11130.1436421577612600.1233023782194929X-RAY DIFFRACTION98.7440532826
2.1113-2.22250.1567179461412600.1238540569034934X-RAY DIFFRACTION99.846212995
2.2225-2.36170.1516604692462620.1238960008394978X-RAY DIFFRACTION99.6197718631
2.3617-2.5440.1472526140872610.1269854015444978X-RAY DIFFRACTION99.6955280685
2.544-2.79980.1682050698492590.1415145038154933X-RAY DIFFRACTION99.0650639191
2.7998-3.20440.1670498745712630.1550616814734986X-RAY DIFFRACTION99.6582494779
3.2044-4.03550.1563774641282600.146796770844955X-RAY DIFFRACTION98.5077446165
4.0355-28.76730.1530842764282660.1522408076885072X-RAY DIFFRACTION98.8518518519

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