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- PDB-6zjk: Ribonucleotide reductase R2 subunit from Clostridium botulinum -

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Basic information

Entry
Database: PDB / ID: 6zjk
TitleRibonucleotide reductase R2 subunit from Clostridium botulinum
ComponentsRibonucleoside-diphosphate reductase subunit beta
KeywordsMETAL BINDING PROTEIN / ribonucleotide / reductase / nucleotide / R2
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / metal ion binding
Similarity search - Function
Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Ribonucleoside-diphosphate reductase subunit beta
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMartinez-Carranza, M. / Stenmark, P.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.
Authors: Martinez-Carranza, M. / Jonna, V.R. / Lundin, D. / Sahlin, M. / Carlson, L.A. / Jemal, N. / Hogbom, M. / Sjoberg, B.M. / Stenmark, P. / Hofer, A.
History
DepositionJun 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 31, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ribonucleoside-diphosphate reductase subunit beta
A: Ribonucleoside-diphosphate reductase subunit beta
D: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,80116
Polymers172,9864
Non-polymers81512
Water3,477193
1
C: Ribonucleoside-diphosphate reductase subunit beta
D: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9018
Polymers86,4932
Non-polymers4086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-69 kcal/mol
Surface area23960 Å2
MethodPISA
2
A: Ribonucleoside-diphosphate reductase subunit beta
B: Ribonucleoside-diphosphate reductase subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9018
Polymers86,4932
Non-polymers4086
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6780 Å2
ΔGint-73 kcal/mol
Surface area24240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.827, 61.854, 154.342
Angle α, β, γ (deg.)90.000, 127.460, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-544-

HOH

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Components

#1: Protein
Ribonucleoside-diphosphate reductase subunit beta


Mass: 43246.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (strain Loch Maree / Type A3) (bacteria)
Strain: Loch Maree / Type A3 / Gene: nrdB, CLK_2200 / Production host: Escherichia coli (E. coli)
References: UniProt: B1KYY8, ribonucleoside-diphosphate reductase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / Details: sodium bromide, Bis Tris propane pH 6.5, PEG 3350

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Data collection

DiffractionMean temperature: 115 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionLimit h max: 99 / Limit h min: -103 / Limit k max: 19 / Limit k min: -20 / Limit l max: 75 / Limit l min: -74 / Number: 123556 / Theta max: 13.345875285 ° / Theta min: 0.544372704633 °
ReflectionResolution: 2→83.68 Å / Num. obs: 106664 / % possible obs: 99.6 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.71
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 7815 / CC1/2: 0.664
Cell measurementReflection used: 123556 / Theta max: 13.345875285 ° / Theta min: 0.544372704633 °

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Processing

Software
NameVersionClassification
DIALSdata reduction
xia2data scaling
PHENIX1.18rc4-3812-000refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2RCC

2rcc


Resolution: 2→83.67 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 5455 5.16 %
Rwork0.222 --
obs0.2227 105789 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.08 Å2 / Biso mean: 54.6969 Å2 / Biso min: 31.96 Å2
Refinement stepCycle: final / Resolution: 2→83.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10647 0 32 193 10872
Biso mean--52.28 50.86 -
Num. residues----1264
Refinement TLS params.Method: refined / Origin x: -7.0152 Å / Origin y: 15.2283 Å / Origin z: 32.2143 Å
111213212223313233
T0.2414 Å2-0.011 Å2-0.0052 Å2-0.6355 Å20.0538 Å2--0.3163 Å2
L0.6359 °2-0.2452 °2-0.3285 °2-0.2352 °20.2786 °2--0.799 °2
S0.0859 Å °0.0418 Å °0.1065 Å °-0.0592 Å °-0.0187 Å °-0.0591 Å °-0.0239 Å °-0.0303 Å °-0.0734 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allC0 - 315
2X-RAY DIFFRACTION1allA-1 - 315
3X-RAY DIFFRACTION1allD1 - 315
4X-RAY DIFFRACTION1allB0 - 315
5X-RAY DIFFRACTION1allF1 - 5
6X-RAY DIFFRACTION1allE1 - 197
7X-RAY DIFFRACTION1allG1 - 8

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