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

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Basic information

Entry
Database: PDB / ID: 6tqx
TitleCrystal structure of apo (metal-free) ribonucleotide reductase NrdF L61G variant 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 / membrane / metal ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily ...Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / 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: 2.05001760485 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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)74,5768
Polymers74,0002
Non-polymers5766
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-116 kcal/mol
Surface area21410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.335, 60.493, 95.601
Angle α, β, γ (deg.)90.000, 106.623, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETLYSLYS(chain 'A' and (resid 1 through 98 or resid 100...AA1 - 981 - 98
12TYRTYRALAALA(chain 'A' and (resid 1 through 98 or resid 100...AA100 - 156100 - 156
13VALVALGLNGLN(chain 'A' and (resid 1 through 98 or resid 100...AA158 - 208158 - 208
14PHEPHEGLUGLU(chain 'A' and (resid 1 through 98 or resid 100...AA210 - 275210 - 275
15ILEILEARGARG(chain 'A' and (resid 1 through 98 or resid 100...AA279 - 288279 - 288
26METMETLYSLYS(chain 'B' and (resid 1 through 98 or resid 100...BB1 - 981 - 98
27TYRTYRALAALA(chain 'B' and (resid 1 through 98 or resid 100...BB100 - 156100 - 156
28VALVALGLNGLN(chain 'B' and (resid 1 through 98 or resid 100...BB158 - 208158 - 208
29PHEPHEGLUGLU(chain 'B' and (resid 1 through 98 or resid 100...BB210 - 275210 - 275
210ILEILEARGARG(chain 'B' and (resid 1 through 98 or resid 100...BB279 - 288279 - 288

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Components

#1: Protein Ribonucleoside-diphosphate reductase subunit beta


Mass: 36999.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: L61G variant / Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: nrdF, GBAA_1372 / Variant: pXO1-/pXO2- deficient / Cell line (production host): Rosetta 2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q81TB4, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.15 Å3/Da / Density % sol: 42.7 %
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: ESRF / Beamline: ID23-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.05→54.49 Å / Num. obs: 38704 / % possible obs: 98 % / Redundancy: 3 % / Biso Wilson estimate: 23.316304141 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.077 / Rrim(I) all: 0.11 / Net I/σ(I): 6.5
Reflection shellResolution: 2.05→2.12 Å / Rmerge(I) obs: 0.39 / Num. unique obs: 3903 / CC1/2: 0.902 / Rpim(I) all: 0.377 / Rrim(I) all: 0.543

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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: 2.05001760485→54.4899451829 Å / SU ML: 0.220428032838 / Cross valid method: FREE R-VALUE / σ(F): 0.972237341749 / Phase error: 22.7204860904
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.207177922313 1889 4.89758879959 %Random selection
Rwork0.168044694115 36681 --
obs0.17000416367 38570 97.3940710065 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.3246644965 Å2
Refinement stepCycle: LAST / Resolution: 2.05001760485→54.4899451829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4608 0 30 250 4888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01185991943984754
X-RAY DIFFRACTIONf_angle_d1.100406507866431
X-RAY DIFFRACTIONf_chiral_restr0.0570031021853711
X-RAY DIFFRACTIONf_plane_restr0.00710737625101812
X-RAY DIFFRACTIONf_dihedral_angle_d18.8602959231745
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05001760485-2.10540.2779461555341590.2272308961992804X-RAY DIFFRACTION98.667998668
2.1054-2.16740.2346877784951450.2015134222232862X-RAY DIFFRACTION98.881946728
2.1674-2.23740.2140248273521470.1753974428182825X-RAY DIFFRACTION97.6346911958
2.2374-2.31730.1978361361251530.1705234824242792X-RAY DIFFRACTION97.6458885942
2.3173-2.41010.2220171409611460.1705003415072740X-RAY DIFFRACTION95.1219512195
2.4101-2.51980.2309516476351390.1630511202152809X-RAY DIFFRACTION97.1014492754
2.5198-2.65260.2233623218031440.1543880276652830X-RAY DIFFRACTION98.8368228647
2.6526-2.81880.2225608876541490.1654953812022846X-RAY DIFFRACTION98.5521553142
2.8188-3.03650.1943768614551290.1632899247122828X-RAY DIFFRACTION97.2057856673
3.0365-3.3420.223282115291310.169764390232823X-RAY DIFFRACTION96.3784665579
3.342-3.82550.171978704271240.1484268766632897X-RAY DIFFRACTION98.8223748773
3.8255-4.81920.1685748753651570.1430294596232805X-RAY DIFFRACTION96.5449804433
4.8192-54.48994518290.2200548805761660.1980921916382820X-RAY DIFFRACTION94.9141767324

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