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- PDB-6qo8: Crystal structure of ribonucleotide reductase NrdF from Bacillus ... -

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Basic information

Entry
Database: PDB / ID: 6qo8
TitleCrystal structure of ribonucleotide reductase NrdF from Bacillus anthracis anaerobically soaked with ferrous 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: 1.31921770161 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 / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _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)75,02512
Polymers74,1122
Non-polymers91310
Water9,836546
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-102 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.558, 61.456, 95.794
Angle α, β, γ (deg.)90.000, 106.589, 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / 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: 2.19 Å3/Da / Density % sol: 43.86 %
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: 1.319→45.903 Å / Num. obs: 147577 / % possible obs: 97.86 % / Redundancy: 3.2 % / Biso Wilson estimate: 12.7813381668 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.026 / Rrim(I) all: 0.048 / Net I/σ(I): 14.7
Reflection shellResolution: 1.319→1.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 13178 / CC1/2: 0.817 / Rpim(I) all: 0.343 / Rrim(I) all: 0.559 / % possible all: 87.89

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Processing

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

6qo5


Resolution: 1.31921770161→45.9034025688 Å / SU ML: 0.108767294041 / Cross valid method: FREE R-VALUE / σ(F): 1.35846052973 / Phase error: 15.0212539842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.160607752928 7360 4.99799672686 %Random selection
Rwork0.133724482784 139899 --
obs0.135057759383 147259 97.8315606253 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.2211682502 Å2
Refinement stepCycle: LAST / Resolution: 1.31921770161→45.9034025688 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4648 0 43 546 5237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0108046113914928
X-RAY DIFFRACTIONf_angle_d1.135186387256692
X-RAY DIFFRACTIONf_chiral_restr0.0783704317059737
X-RAY DIFFRACTIONf_plane_restr0.0076840154793853
X-RAY DIFFRACTIONf_dihedral_angle_d21.40035678221824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3192-1.33420.2611896533992010.2242803080913831X-RAY DIFFRACTION80.0158761659
1.3342-1.34990.2301536959322250.2051281333984269X-RAY DIFFRACTION90.6596731894
1.3499-1.36640.2301206940682310.2097405477014408X-RAY DIFFRACTION92.8914697637
1.3664-1.38370.276256214192300.2059731863614345X-RAY DIFFRACTION91.7385201524
1.3837-1.40190.2041758923892510.1705209988754769X-RAY DIFFRACTION99.7615262321
1.4019-1.42110.1932105809552470.1543189813944699X-RAY DIFFRACTION99.9191919192
1.4211-1.44140.1845219912542490.1545786068544723X-RAY DIFFRACTION99.5594713656
1.4414-1.46290.1919132584272470.149139361044685X-RAY DIFFRACTION98.5611510791
1.4629-1.48580.1865936596082430.1405764065734648X-RAY DIFFRACTION98.0356784927
1.4858-1.51010.1563335991722490.1236394115534746X-RAY DIFFRACTION99.7005988024
1.5101-1.53620.1709923602872440.1291449637324641X-RAY DIFFRACTION97.3107569721
1.5362-1.56410.1459601996872500.1146377398814728X-RAY DIFFRACTION99.6995794112
1.5641-1.59420.1467370837762480.1022617772724721X-RAY DIFFRACTION99.9195656545
1.5942-1.62670.1291077536822500.1002648360764749X-RAY DIFFRACTION99.8601677986
1.6267-1.66210.1598385619522490.1060212879874753X-RAY DIFFRACTION99.8403193613
1.6621-1.70080.1276215278212490.106891627574755X-RAY DIFFRACTION99.7011356844
1.7008-1.74330.1639852079662490.106931388594725X-RAY DIFFRACTION99.3607670795
1.7433-1.79040.1406148382942510.1092946587234760X-RAY DIFFRACTION99.8406056983
1.7904-1.84310.139686484512490.1069517215154730X-RAY DIFFRACTION99.7995590299
1.8431-1.90260.144731429612460.1153766548224696X-RAY DIFFRACTION98.7807315611
1.9026-1.97060.1556693118062460.1206314373434671X-RAY DIFFRACTION97.9677226539
1.9706-2.04950.150116832382530.1200968792394793X-RAY DIFFRACTION99.6642306933
2.0495-2.14280.1447871365892450.1219214962474678X-RAY DIFFRACTION98.696872494
2.1428-2.25580.1330970064782480.115193027544720X-RAY DIFFRACTION99.3798759752
2.2558-2.39710.129264459622510.1176709673854768X-RAY DIFFRACTION99.1701244813
2.3971-2.58210.152167768042500.1223495258114746X-RAY DIFFRACTION99.6807661612
2.5821-2.8420.1621070759442510.1396561588684768X-RAY DIFFRACTION99.1113744076
2.842-3.25310.1785052965942510.1488216231624783X-RAY DIFFRACTION99.3487270574
3.2531-4.09820.153385910482510.1415273084134755X-RAY DIFFRACTION98.4657749803
4.0982-45.93120.183898772242560.1579510694844836X-RAY DIFFRACTION98.4912959381

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