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

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Basic information

Entry
Database: PDB / ID: 6tqv
TitleCrystal structure of ribonucleotide reductase NrdF from Bacillus anthracis aerobically soaked with Fe(II) and Mn(II) 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 str. Sterne (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35000968892 Å
AuthorsGrave, K. / Hogbom, M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2020
Title: The Bacillus anthracis class Ib ribonucleotide reductase subunit NrdF intrinsically selects manganese over iron.
Authors: Grave, K. / Griese, J.J. / Berggren, G. / Bennett, M.D. / Hogbom, M.
History
DepositionDec 17, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 3, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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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)74,81211
Polymers74,1122
Non-polymers7009
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-103 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.178, 60.300, 95.831
Angle α, β, γ (deg.)90.000, 106.469, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 str. Sterne (bacteria)
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-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 353 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.46 %
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: SLS / Beamline: X06SA / Wavelength: 1.04 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.35→54.3536195985 Å / Num. obs: 131966 / % possible obs: 96.05 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.6832569535 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.036 / Rpim(I) all: 0.032 / Rrim(I) all: 0.049 / Net I/σ(I): 12.3
Reflection shellResolution: 1.35→1.39 Å / Rmerge(I) obs: 0.589 / Num. unique obs: 11538 / CC1/2: 0.629 / Rpim(I) all: 0.548 / Rrim(I) all: 0.803

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QO9

6qo9


Resolution: 1.35000968892→54.3536195985 Å / SU ML: 0.121453353802 / Cross valid method: FREE R-VALUE / σ(F): 1.97180886301 / Phase error: 17.5972998692
RfactorNum. reflection% reflectionSelection details
Rfree0.168876487598 6665 5 %Random selection
Rwork0.146570980629 ---
obs0.147741493981 131718 96.0491774589 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.1813998233 Å2
Refinement stepCycle: LAST / Resolution: 1.35000968892→54.3536195985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4625 0 29 353 5007
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0101308721744798
X-RAY DIFFRACTIONf_angle_d1.093605428796497
X-RAY DIFFRACTIONf_chiral_restr0.0755164168085721
X-RAY DIFFRACTIONf_plane_restr0.00767919786451823
X-RAY DIFFRACTIONf_dihedral_angle_d24.1152680221767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35000968892-1.36540.3033126692111590.2499431020153430X-RAY DIFFRACTION78.055676381
1.3654-1.38140.2692085286581870.2350297603223585X-RAY DIFFRACTION84.2340330505
1.3814-1.39830.2465670847582160.2183606507323931X-RAY DIFFRACTION90.6844522195
1.3983-1.4160.2267852639892150.2048521294324215X-RAY DIFFRACTION97.4697469747
1.416-1.43460.2184965740542450.1896247056244255X-RAY DIFFRACTION97.9538528515
1.4346-1.45430.2007970808212490.1815673340944159X-RAY DIFFRACTION97.9337924906
1.4543-1.4750.2329564306432220.1726099185814203X-RAY DIFFRACTION97.4240422721
1.475-1.4970.1799934709222160.1583035647494208X-RAY DIFFRACTION97.0814132104
1.497-1.52040.1922255326172140.152763409444183X-RAY DIFFRACTION96.5100965759
1.5204-1.54540.1722426553822230.1501326654014115X-RAY DIFFRACTION94.612868048
1.5454-1.5720.1844927190372420.143712037633923X-RAY DIFFRACTION92.044198895
1.572-1.60060.1556671644562050.1357212289634272X-RAY DIFFRACTION98.6557955046
1.6006-1.63140.1699281973622180.136950513634320X-RAY DIFFRACTION98.673624701
1.6314-1.66470.1784608096132210.1373791976514254X-RAY DIFFRACTION98.2652613087
1.6647-1.70090.1748092991412230.1330880468094216X-RAY DIFFRACTION97.9695431472
1.7009-1.74050.1660674637751910.129508857394259X-RAY DIFFRACTION97.6948408342
1.7405-1.7840.1646479407171880.1215165785224233X-RAY DIFFRACTION96.7819614711
1.784-1.83220.1416014534582110.1239787145214043X-RAY DIFFRACTION93.4329013837
1.8322-1.88610.1585829347032270.1271593485194237X-RAY DIFFRACTION97.3185088293
1.8861-1.9470.1829699787642250.1281198202574305X-RAY DIFFRACTION99.4729907773
1.947-2.01660.1571482635882550.1268172061294300X-RAY DIFFRACTION99.1294885745
2.0166-2.09740.1645641297042320.1254325631284222X-RAY DIFFRACTION98.3874530594
2.0974-2.19280.1492614216522380.1256523495834249X-RAY DIFFRACTION97.289679098
2.1928-2.30840.1605418214562210.1289595668064121X-RAY DIFFRACTION94.7001090513
2.3084-2.45310.1366649023112290.1281811022714258X-RAY DIFFRACTION98.3128834356
2.4531-2.64250.1644944665812140.133938035474332X-RAY DIFFRACTION99.3661202186
2.6425-2.90840.1569289519662490.1425082183694314X-RAY DIFFRACTION99.1956521739
2.9084-3.32920.1678224069952590.1560633297754217X-RAY DIFFRACTION96.4655172414
3.3292-4.19420.1542495335162260.1457925467294348X-RAY DIFFRACTION99.0043290043
4.1942-54.35361959850.1807906037762450.1781713299364346X-RAY DIFFRACTION97.2051662079

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