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- PDB-6tqz: Crystal structure of ribonucleotide reductase NrdF L61G variant f... -

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Basic information

Entry
Database: PDB / ID: 6tqz
TitleCrystal structure of ribonucleotide reductase NrdF L61G variant 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 (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09933498464 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_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

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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)74,79812
Polymers74,0002
Non-polymers79810
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-116 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.019, 60.124, 96.048
Angle α, β, γ (deg.)90.000, 106.593, 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: 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 / 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.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.13 Å3/Da / Density % sol: 42.31 %
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: 14.2 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.09933498464→46.0241591744 Å / Num. obs: 36123 / % possible obs: 98.21 % / Redundancy: 3.8 % / Biso Wilson estimate: 25.4255784597 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.0523 / Rrim(I) all: 0.104 / Net I/σ(I): 9.4
Reflection shellResolution: 2.09933498464→2.17 Å / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 3 / Num. unique obs: 3585 / CC1/2: 0.928 / Rpim(I) all: 0.221 / Rrim(I) all: 0.444

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Processing

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

6qo9


Resolution: 2.09933498464→46.0241591744 Å / SU ML: 0.206340402728 / Cross valid method: FREE R-VALUE / σ(F): 1.36588380498 / Phase error: 23.2500349398
RfactorNum. reflection% reflectionSelection details
Rfree0.22166196209 1799 4.99375433727 %Random selection
Rwork0.16581837594 ---
obs0.168555209604 36025 98.2249972734 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.3836930735 Å2
Refinement stepCycle: LAST / Resolution: 2.09933498464→46.0241591744 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4622 0 34 208 4864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01154137930074739
X-RAY DIFFRACTIONf_angle_d1.062393037626407
X-RAY DIFFRACTIONf_chiral_restr0.0520246249399708
X-RAY DIFFRACTIONf_plane_restr0.00622084122609809
X-RAY DIFFRACTIONf_dihedral_angle_d16.99674731561737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09933498464-2.15610.2431211772211370.186811470882603X-RAY DIFFRACTION97.1631205674
2.1561-2.21950.2360977495851380.1707362853772648X-RAY DIFFRACTION99.0753911807
2.2195-2.29120.2368921737451390.1681784802862628X-RAY DIFFRACTION99.0691013247
2.2912-2.37310.2158290923631390.1639605516432640X-RAY DIFFRACTION99.1084165478
2.3731-2.46810.2580827420611360.1706748853732589X-RAY DIFFRACTION97.600286533
2.4681-2.58040.2452608034061320.1692396496872520X-RAY DIFFRACTION94.4108223567
2.5804-2.71640.2141977846361400.164059647252659X-RAY DIFFRACTION99.3610223642
2.7164-2.88660.2536313095881380.1741528064732640X-RAY DIFFRACTION99.6055934027
2.8866-3.10940.2369756694041400.1772798379292658X-RAY DIFFRACTION99.6793729961
3.1094-3.42220.215772446341410.174189902572687X-RAY DIFFRACTION99.5073891626
3.4222-3.91720.1926295283241400.1470487238242660X-RAY DIFFRACTION99.0799716914
3.9172-4.93440.1775385570271360.1443427543262578X-RAY DIFFRACTION95.39543058
4.9344-46.02415917440.2505286093541430.182298622332716X-RAY DIFFRACTION97.9780671693

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