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- PDB-6qrz: Crystal structure of R2-like ligand-binding oxidase from Sulfolob... -

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Basic information

Entry
Database: PDB / ID: 6qrz
TitleCrystal structure of R2-like ligand-binding oxidase from Sulfolobus acidocaldarius solved by 3D micro-crystal electron diffraction
ComponentsRibonucleoside-diphosphate reductaseRibonucleotide reductase
KeywordsOXIDOREDUCTASE / micro-crystal / microED / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN OXIDOREDUCTASE / FERRITIN-LIKE SUPERFAMILY
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process
Similarity search - Function
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
: / MANGANESE (III) ION / Ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodELECTRON CRYSTALLOGRAPHY / electron crystallography / cryo EM / Resolution: 3 Å
AuthorsXu, H. / Lebrette, H. / Clabbers, M.T.B. / Zhao, J. / Griese, J.J. / Zou, X. / Hogbom, M.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2017-04018 Sweden
Knut and Alice Wallenberg FoundationWallenberg Academy Fellows 2017.0275 Sweden
Knut and Alice Wallenberg Foundation3DEM-NATUR 2012.0112 Sweden
Swedish Research CouncilVR Starting Grant 2017-05333 Sweden
Citation
Journal: Sci Adv / Year: 2019
Title: Solving a new R2lox protein structure by microcrystal electron diffraction.
Authors: Hongyi Xu / Hugo Lebrette / Max T B Clabbers / Jingjing Zhao / Julia J Griese / Xiaodong Zou / Martin Högbom /
Abstract: Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be ...Microcrystal electron diffraction (MicroED) has recently shown potential for structural biology. It enables the study of biomolecules from micrometer-sized 3D crystals that are too small to be studied by conventional x-ray crystallography. However, to date, MicroED has only been applied to redetermine protein structures that had already been solved previously by x-ray diffraction. Here, we present the first new protein structure-an R2lox enzyme-solved using MicroED. The structure was phased by molecular replacement using a search model of 35% sequence identity. The resulting electrostatic scattering potential map at 3.0-Å resolution was of sufficient quality to allow accurate model building and refinement. The dinuclear metal cofactor could be located in the map and was modeled as a heterodinuclear Mn/Fe center based on previous studies. Our results demonstrate that MicroED has the potential to become a widely applicable tool for revealing novel insights into protein structure and function.
#1: Journal: Biorxiv / Year: 2019
Title: Solving the first novel protein structure by 3D micro-crystal electron diffraction
Authors: Xu, H. / Lebrette, H. / Clabbers, M.T.B. / Zhao, J. / Griese, J.J. / Zou, X. / Hogbom, M.
History
DepositionFeb 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author / em_image_scans
Revision 1.2Sep 11, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1693
Polymers38,0591
Non-polymers1112
Water0
1
A: Ribonucleoside-diphosphate reductase
hetero molecules

A: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3396
Polymers76,1172
Non-polymers2224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5360 Å2
ΔGint-67 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.310, 108.930, 48.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Ribonucleoside-diphosphate reductase / Ribonucleotide reductase


Mass: 38058.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: Saci_2188 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q4J6V7, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-MN3 / MANGANESE (III) ION / Manganese


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe

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Experimental details

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Experiment

ExperimentMethod: ELECTRON CRYSTALLOGRAPHY
EM experimentAggregation state: 3D ARRAY / 3D reconstruction method: electron crystallography

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Sample preparation

ComponentName: R2-like ligand-binding oxidase / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Sulfolobus acidocaldarius DSM 639 (acidophilic)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 3.4
Buffer component
IDConc.NameFormulaBuffer-ID
144 %(w/v)polyethylene glycol 4001
20.2 Mlithium sulfateLi2SO41
30.1 Msodium acetateC2H3NaO21
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Plate-like micro-crystals grow within 48h at 21C by hanging drop vapour diffusion
VitrificationCryogen name: ETHANE

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Data collection

MicroscopyModel: JEOL 2100
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DIFFRACTION / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN
Specimen holder model: GATAN 914 HIGH TILT LIQUID NITROGEN CRYO TRANSFER TOMOGRAPHY HOLDER
Image recordingElectron dose: 0.16 e/Å2 / Film or detector model: OTHER
EM diffractionCamera length: 1830 mm
EM diffraction shellResolution: 29→3 Å / Fourier space coverage: 62.8 % / Multiplicity: 32.4 / Num. of structure factors: 4452 / Phase residual: 1 °
EM diffraction statsFourier space coverage: 62.8 % / High resolution: 3 Å / Num. of intensities measured: 144428 / Num. of structure factors: 4452 / Phase error: 0 ° / Phase residual: 1 ° / Phase error rejection criteria: 0 / Rmerge: 0.553 / Rsym: 0.553

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.2phasing
Coot0.8.9model building
EM software
IDNameCategory
6Cootmodel fitting
13PHENIXmodel refinement
EM 3D crystal entity∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 63.305 Å / B: 108.925 Å / C: 48.165 Å / Space group name: P21212 / Space group num: 18
CTF correctionType: NONE
3D reconstructionResolution: 3 Å / Resolution method: DIFFRACTION PATTERN/LAYERLINES / Symmetry type: 3D CRYSTAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL
Atomic model buildingPDB-ID: 3EE4

3ee4


Pdb chain-ID: A
RefinementResolution: 3→28.995 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.07
RfactorNum. reflection% reflection
Rfree0.3347 233 5.27 %
Rwork0.3179 --
obs0.3189 4423 62.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON CRYSTALLOGRAPHYf_bond_d0.0022293
ELECTRON CRYSTALLOGRAPHYf_angle_d0.4113104
ELECTRON CRYSTALLOGRAPHYf_dihedral_angle_d6.5461376
ELECTRON CRYSTALLOGRAPHYf_chiral_restr0.035345
ELECTRON CRYSTALLOGRAPHYf_plane_restr0.003391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0003-3.77870.4131960.38541943ELECTRON CRYSTALLOGRAPHY59
3.7787-28.99650.30561370.28882247ELECTRON CRYSTALLOGRAPHY66

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