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

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Basic information

Entry
Database: PDB / ID: 7bet
TitleStructure of Ribonucleotide reductase R2 from Escherichia coli collected by femtosecond serial crystallography on a COC membrane
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 small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsAurelius, O. / John, J. / Martiel, I. / Marsh, M. / Vera, L. / Huang, C.Y. / Olieric, V. / Leonarski, P. / Nass, K. / Padeste, C. ...Aurelius, O. / John, J. / Martiel, I. / Marsh, M. / Vera, L. / Huang, C.Y. / Olieric, V. / Leonarski, P. / Nass, K. / Padeste, C. / Karpik, A. / Hogbom, M. / Wang, M. / Pedrini, B.
Funding support Sweden, European Union, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg Foundation Sweden
European Research Council (ERC)HIGH-GEAR 724394European Union
CitationJournal: To Be Published
Title: Commissioning results from the SwissMX instrument for fixed target macromolecular crystallography at SwissFEL
Authors: Martiel, I. / Pradervand, C. / Panepucci, E. / Zamofing, T. / Nass, K. / Marsh, M. / Vera, L. / Hunag, C.Y. / Olieric, V. / Buntschu, D. / Kaelin, R. / Leonarski, P. / Ozerov, D. / Padeste, ...Authors: Martiel, I. / Pradervand, C. / Panepucci, E. / Zamofing, T. / Nass, K. / Marsh, M. / Vera, L. / Hunag, C.Y. / Olieric, V. / Buntschu, D. / Kaelin, R. / Leonarski, P. / Ozerov, D. / Padeste, C. / Karpik, A. / Thominet, V. / Hora, J. / Olieric, N. / Weinert, T. / Wranik, M. / Brunle, S. / Standfuss, J. / Aurelius, O. / John, J. / Hogbom, M. / Zhang, L. / Einsle, O. / Papp, G. / Basu, S. / Cipriani, F. / Beaud, P. / Mankowsky, R. / Glettig, W. / Mozzanica, A. / Redford, S. / Schmidt, B. / Bunk, O. / Abela, R. / Wang, M. / Lemke, H. / Pedrini, B.
History
DepositionDec 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 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
Water1,20767
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 area6330 Å2
ΔGint-61 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.600, 91.600, 207.200
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-501-

HOH

21A-513-

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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.88 Å3/Da / Density % sol: 57.3 %
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: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESB / Wavelength: 1.359 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: Mar 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.359 Å / Relative weight: 1
ReflectionResolution: 2.29→19.91 Å / Num. obs: 23626 / % possible obs: 100 % / Redundancy: 175 % / Biso Wilson estimate: 59.66 Å2 / CC1/2: 0.9936 / CC star: 0.9984 / R split: 0.0863 / Net I/σ(I): 6.65
Reflection shellResolution: 2.29→2.33 Å / Mean I/σ(I) obs: 1.27 / Num. unique obs: 1196 / CC1/2: 0.3532 / CC star: 0.7225 / R split: 1.069
Serial crystallography measurementPulse photon energy: 9.12 keV
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetDescription: SwissMX CM / Sample dehydration prevention: cryogenic conditions / Sample holding: COC membrane / Support base: SwissMX goniometer
Serial crystallography data reductionFrames indexed: 7500 / XFEL pulse events: 52300

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Processing

Software
NameVersionClassification
CrystFEL0.7 / 0.8data reduction
CrystFEL0.7 / 0.8data scaling
PHENIX1.18.2_3874refinement
PHASER1.18.2_3874phasing
Coot0.9model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MXR

1mxr


Resolution: 2.3→19.91 Å / SU ML: 0.3007 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.6848
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2451 1182 5 %
Rwork0.2054 22439 -
obs0.2074 23621 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.39 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2781 0 2 67 2850
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032845
X-RAY DIFFRACTIONf_angle_d0.51033859
X-RAY DIFFRACTIONf_chiral_restr0.0382425
X-RAY DIFFRACTIONf_plane_restr0.0031496
X-RAY DIFFRACTIONf_dihedral_angle_d16.16961053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.40.39721450.34392743X-RAY DIFFRACTION100
2.4-2.530.3941430.3262728X-RAY DIFFRACTION100
2.53-2.690.34721460.29732765X-RAY DIFFRACTION99.93
2.69-2.90.36441440.27762747X-RAY DIFFRACTION100
2.9-3.190.30881460.25272783X-RAY DIFFRACTION99.97
3.19-3.650.2221480.20822798X-RAY DIFFRACTION99.97
3.65-4.580.1871500.18512854X-RAY DIFFRACTION99.93
4.58-19.910.22471600.16773021X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -22.399672486 Å / Origin y: 30.188187117 Å / Origin z: 4.69829038065 Å
111213212223313233
T0.827885090031 Å2-0.211626175783 Å20.184419707013 Å2-0.798896623887 Å2-0.105955878564 Å2--0.391406468032 Å2
L1.24395505355 °2-1.0802459809 °2-0.544030129541 °2-3.56458816404 °21.70022280698 °2--2.17298582973 °2
S0.141785606735 Å °-0.176330409133 Å °0.16524568285 Å °-0.917913500938 Å °0.408979310412 Å °-0.473061111366 Å °-0.393099803927 Å °0.427816440944 Å °-0.258586284934 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 339)

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