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

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Basic information

Entry
Database: PDB / ID: 6qob
TitleCrystal structure of ribonucleotide reductase NrdF from Bacillus anthracis with partially oxidised di-iron metallocofactor
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: 1.457 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 / 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_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,23413
Polymers74,1122
Non-polymers1,12211
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-121 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.137, 60.377, 95.758
Angle α, β, γ (deg.)90.00, 106.38, 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#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.: 2 / Source method: isolated from a natural source / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
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: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.457→45.935 Å / Num. obs: 107862 / % possible obs: 98.67 % / Redundancy: 3.4 % / Biso Wilson estimate: 15.6308396798 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.037 / Rrim(I) all: 0.069 / Net I/σ(I): 11.48
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 3 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 1.62 / Num. unique obs: 28884 / CC1/2: 0.746 / Rpim(I) all: 0.399 / Rrim(I) all: 0.71 / % possible all: 89.12

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX(1.12_2829: ???)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QO5

6qo5


Resolution: 1.457→45.935 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.21
RfactorNum. reflection% reflectionSelection details
Rfree0.1936 5391 5 %Random selection
Rwork0.1698 ---
obs0.171 107820 98.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.457→45.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4659 0 57 357 5073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124952
X-RAY DIFFRACTIONf_angle_d1.186722
X-RAY DIFFRACTIONf_dihedral_angle_d20.8691842
X-RAY DIFFRACTIONf_chiral_restr0.082736
X-RAY DIFFRACTIONf_plane_restr0.008859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4568-1.47340.26081220.29982336X-RAY DIFFRACTION68
1.4734-1.49070.3061790.28393392X-RAY DIFFRACTION100
1.4907-1.50890.27271850.26913517X-RAY DIFFRACTION100
1.5089-1.5280.28991760.25123346X-RAY DIFFRACTION100
1.528-1.54810.29211830.25553479X-RAY DIFFRACTION100
1.5481-1.56930.25251810.23733427X-RAY DIFFRACTION100
1.5693-1.59170.24731830.22573472X-RAY DIFFRACTION100
1.5917-1.61550.25641780.21653397X-RAY DIFFRACTION100
1.6155-1.64070.26421820.20843464X-RAY DIFFRACTION100
1.6407-1.66760.2361810.20193441X-RAY DIFFRACTION100
1.6676-1.69640.22531790.20013409X-RAY DIFFRACTION100
1.6964-1.72720.21561840.1933493X-RAY DIFFRACTION100
1.7272-1.76050.22431790.18653391X-RAY DIFFRACTION100
1.7605-1.79640.2191810.18843456X-RAY DIFFRACTION100
1.7964-1.83550.2221820.17643446X-RAY DIFFRACTION100
1.8355-1.87820.22811810.17283436X-RAY DIFFRACTION100
1.8782-1.92510.2031820.16933458X-RAY DIFFRACTION100
1.9251-1.97720.19931810.16753448X-RAY DIFFRACTION99
1.9772-2.03540.19241820.16373446X-RAY DIFFRACTION100
2.0354-2.10110.19781790.16213417X-RAY DIFFRACTION100
2.1011-2.17620.18841820.15743451X-RAY DIFFRACTION100
2.1762-2.26330.17741830.14943479X-RAY DIFFRACTION100
2.2633-2.36630.18281820.1473449X-RAY DIFFRACTION100
2.3663-2.4910.14861830.14413473X-RAY DIFFRACTION100
2.491-2.64710.16171810.14283450X-RAY DIFFRACTION100
2.6471-2.85150.18351840.15533492X-RAY DIFFRACTION100
2.8515-3.13830.17481820.16553450X-RAY DIFFRACTION100
3.1383-3.59230.17311840.15743491X-RAY DIFFRACTION100
3.5923-4.52530.15321830.14253483X-RAY DIFFRACTION100
4.5253-45.95760.20441870.17473540X-RAY DIFFRACTION98

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