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- PDB-7qbp: Crystal structure of R2-like ligand-binding oxidase from Saccharo... -

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Basic information

Entry
Database: PDB / ID: 7qbp
TitleCrystal structure of R2-like ligand-binding oxidase from Saccharopolyspora Erythraea
ComponentsR2-like ligand binding oxidase
KeywordsOXIDOREDUCTASE / R2LOX / R2-LIKE LIGAND-BINDING OXIDASE / MN/FE COFACTOR / RIBONUCLEOTIDE REDUCTASE R2 SUBUNIT FOLD / METALLOPROTEIN / FERRITIN-LIKE SUPERFAMILY
Function / homology
Function and homology information


Oxidoreductases / deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
R2-like ligand binding oxidase / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / MANGANESE (III) ION / PALMITIC ACID / R2-like ligand binding oxidase
Similarity search - Component
Biological speciesSaccharopolyspora erythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsSrinivas, V. / Diamanti, R. / Lebrette, H. / Hogbom, M.
Funding support Sweden, 4items
OrganizationGrant numberCountry
European Research Council (ERC)HIGH-GEAR 724394 Sweden
Swedish Research Council2017-04018 Sweden
Knut and Alice Wallenberg Foundation2017.0275 Sweden
Knut and Alice Wallenberg Foundation2019.0436 Sweden
CitationJournal: Febs Lett. / Year: 2022
Title: Comparative structural analysis provides new insights into the function of R2-like ligand-binding oxidase.
Authors: Diamanti, R. / Srinivas, V. / Johansson, A.I. / Nordstrom, A. / Griese, J.J. / Lebrette, H. / Hogbom, M.
History
DepositionNov 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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: R2-like ligand binding oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7585
Polymers37,2941
Non-polymers4634
Water3,189177
1
A: R2-like ligand binding oxidase
hetero molecules

A: R2-like ligand binding oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,51510
Polymers74,5892
Non-polymers9278
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7840 Å2
ΔGint-90 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.173, 103.173, 61.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-597-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein R2-like ligand binding oxidase / Ribonucleotide reductase R2 subunit homolog / Ribonucleotide reductase small subunit homolog


Mass: 37294.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338) (bacteria)
Strain: ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338
Gene: SACE_0591 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4F7B2, Oxidoreductases

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Non-polymers , 5 types, 181 molecules

#2: Chemical ChemComp-MN3 / MANGANESE (III) ION


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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 200 mM Lithium sulfate, 100 mM Sodium acetate pH 4.6, and 50 % (w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.38→47.05 Å / Num. obs: 68755 / % possible obs: 99.99 % / Redundancy: 26.1 % / Biso Wilson estimate: 19.07 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06269 / Rrim(I) all: 0.06397 / Net I/σ(I): 29.88
Reflection shellResolution: 1.38→1.429 Å / Rmerge(I) obs: 1.782 / Mean I/σ(I) obs: 1.79 / Num. unique obs: 6772 / CC1/2: 0.755 / Rrim(I) all: 1.818 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EE4

3ee4


Resolution: 1.38→47.05 Å / SU ML: 0.1425 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.1908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1654 3438 5 %
Rwork0.1515 65317 -
obs0.1522 68755 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.33 Å2
Refinement stepCycle: LAST / Resolution: 1.38→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 25 177 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01792449
X-RAY DIFFRACTIONf_angle_d1.38283328
X-RAY DIFFRACTIONf_chiral_restr0.1049344
X-RAY DIFFRACTIONf_plane_restr0.0162447
X-RAY DIFFRACTIONf_dihedral_angle_d14.36912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.40.29251350.27242559X-RAY DIFFRACTION98.43
1.4-1.420.28321340.22652546X-RAY DIFFRACTION100
1.42-1.440.26251350.21462578X-RAY DIFFRACTION100
1.44-1.460.23021360.18762587X-RAY DIFFRACTION100
1.46-1.490.20231350.17322562X-RAY DIFFRACTION100
1.49-1.510.20441360.17192590X-RAY DIFFRACTION100
1.51-1.540.19681380.17642617X-RAY DIFFRACTION100
1.54-1.570.21591340.18922541X-RAY DIFFRACTION100
1.57-1.60.19391370.17772594X-RAY DIFFRACTION100
1.6-1.630.19081360.16012585X-RAY DIFFRACTION100
1.63-1.670.17421360.15222585X-RAY DIFFRACTION100
1.67-1.710.1751360.1452597X-RAY DIFFRACTION100
1.71-1.760.1851370.13912594X-RAY DIFFRACTION100
1.76-1.810.13611370.13412612X-RAY DIFFRACTION100
1.81-1.870.16361370.14692591X-RAY DIFFRACTION100
1.87-1.940.1991370.15632611X-RAY DIFFRACTION100
1.94-2.020.16051360.14652588X-RAY DIFFRACTION100
2.02-2.110.15511390.13442632X-RAY DIFFRACTION100
2.11-2.220.15831380.12792620X-RAY DIFFRACTION100
2.22-2.360.14131380.13252628X-RAY DIFFRACTION100
2.36-2.540.15031380.13442623X-RAY DIFFRACTION100
2.54-2.80.16961400.14212662X-RAY DIFFRACTION100
2.8-3.20.15621400.16132652X-RAY DIFFRACTION100
3.2-4.030.17651420.14742708X-RAY DIFFRACTION100
4.03-47.050.14281510.16042855X-RAY DIFFRACTION100

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