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- PDB-7ai8: Structure of Ribonucleotide reductase R2 from Escherichia coli co... -

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Basic information

Entry
Database: PDB / ID: 7ai8
TitleStructure of Ribonucleotide reductase R2 from Escherichia coli collected by still serial crystallography on a COC membrane at a synchrotron source
ComponentsRibonucleoside-diphosphate reductase 1 subunit beta
KeywordsOXIDOREDUCTASE / metalloprotein
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
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 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsAurelius, O. / John, J. / Martiel, I. / Padeste, C. / Karpik, A. / Huang, C.Y. / Hogbom, M. / Wang, M. / Marsh, M.
Funding support Sweden, European Union, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
European Research Council (ERC)HIGH-GEAR 724394European Union
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Versatile microporous polymer-based supports for serial macromolecular crystallography.
Authors: Martiel, I. / Beale, J.H. / Karpik, A. / Huang, C.Y. / Vera, L. / Olieric, N. / Wranik, M. / Tsai, C.J. / Muhle, J. / Aurelius, O. / John, J. / Hogbom, M. / Wang, M. / Marsh, M. / Padeste, C.
History
DepositionSep 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 29, 2021Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6703
Polymers43,5581
Non-polymers1122
Water1,856103
1
A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules

A: Ribonucleoside-diphosphate reductase 1 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3396
Polymers87,1162
Non-polymers2234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area6660 Å2
ΔGint-81 kcal/mol
Surface area23490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.350, 90.350, 208.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-585-

HOH

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Components

#1: Protein Ribonucleoside-diphosphate reductase 1 subunit beta / Protein B2 / Protein R2 / Ribonucleotide reductase 1


Mass: 43558.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: nrdB, ftsB, b2235, JW2229 / Production host: Escherichia coli (E. coli)
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 34-37 % PAA 2100, 100 mM HEPES 7.0, 250-450 mM NaCl, 200 mM ammonium sulfate [and] 26% PAA 2100, 100 mM HEPES 7.0, 150 NaCl, 100 Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.08→52.2 Å / Num. obs: 31083 / % possible obs: 99.65 % / Redundancy: 201.59 % / Biso Wilson estimate: 41.87 Å2 / CC1/2: 0.9967 / CC star: 0.9992 / R split: 0.0538 / Net I/σ(I): 10.74
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 1.74 / Num. unique obs: 1474 / CC1/2: 0.3829 / CC star: 0.7441 / R split: 0.7483 / % possible all: 96.66
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample holding: COC thin membrane

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Processing

Software
NameVersionClassification
CrystFEL0.7 / 0.8data reduction
CrystFEL0.7 / 0.8data scaling
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874phasing
Coot0.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXR

1mxr


Resolution: 2.1→51.97 Å / SU ML: 0.2272 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.9367
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2192 1505 5 %
Rwork0.19 28589 -
obs0.1914 30094 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.43 Å2
Refinement stepCycle: LAST / Resolution: 2.1→51.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 2 103 2886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00692858
X-RAY DIFFRACTIONf_angle_d0.83063879
X-RAY DIFFRACTIONf_chiral_restr0.0455427
X-RAY DIFFRACTIONf_plane_restr0.005499
X-RAY DIFFRACTIONf_dihedral_angle_d22.77011063
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.170.35161300.31282463X-RAY DIFFRACTION97.66
2.17-2.250.29051320.26222527X-RAY DIFFRACTION99.07
2.25-2.340.26361340.23232539X-RAY DIFFRACTION99.33
2.34-2.440.28461330.22382571X-RAY DIFFRACTION99.52
2.44-2.570.26881360.20562549X-RAY DIFFRACTION99.78
2.57-2.730.22571350.20082570X-RAY DIFFRACTION99.74
2.73-2.940.27831360.20822589X-RAY DIFFRACTION100
2.94-3.240.21541380.20272617X-RAY DIFFRACTION99.82
3.24-3.710.2131370.19072607X-RAY DIFFRACTION99.82
3.71-4.670.17631430.15822688X-RAY DIFFRACTION99.89
4.67-51.970.19891510.17352869X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -21.6870560366 Å / Origin y: 29.9104760991 Å / Origin z: 4.74723600776 Å
111213212223313233
T0.58939514316 Å2-0.0814174462062 Å20.146638627644 Å2-0.526722259698 Å2-0.0813009001411 Å2--0.326226468233 Å2
L0.909782715693 °2-0.609732530918 °2-0.339962291214 °2-2.10264206161 °20.721131114001 °2--1.5902201617 °2
S0.0843683493787 Å °-0.0754490865709 Å °0.191436062487 Å °-0.480872376359 Å °0.248750609397 Å °-0.456703427797 Å °-0.224170580876 Å °0.225657690653 Å °-0.267626676632 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 339)

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