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- PDB-7qbk: Crystal structure of a second homolog of R2-like ligand-binding o... -

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Basic information

Entry
Database: PDB / ID: 7qbk
TitleCrystal structure of a second homolog of R2-like ligand-binding oxidase in Sulfolobus acidocaldarius (SaR2loxII)
ComponentsR2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius
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


deoxyribonucleotide biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily
Similarity search - Domain/homology
: / MANGANESE (III) ION / Uncharacterized protein
Similarity search - Component
Biological speciesSulfolobus acidocaldarius DSM 639 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsLebrette, H. / Diamanti, R. / Srinivas, V. / 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

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Assembly

Deposited unit
A: R2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1713
Polymers37,0611
Non-polymers1112
Water95553
1
A: R2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius
hetero molecules

A: R2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3436
Polymers74,1212
Non-polymers2224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z1
Buried area3110 Å2
ΔGint-56 kcal/mol
Surface area23170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.029, 128.029, 41.894
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64
Space group name HallP64
Symmetry operation#1: x,y,z
#2: x-y,x,z+2/3
#3: y,-x+y,z+1/3
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z

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Components

#1: Protein R2-like ligand-binding oxidase (homolog II) from Sulfolobus acidocaldarius


Mass: 37060.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius DSM 639 (acidophilic)
Gene: Saci_1112 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4J9R6
#2: Chemical ChemComp-MN3 / MANGANESE (III) ION


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


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 24% (w/v) polyethylene glycol 1500, 5% (v/v) formamide, 40 mM sodium propionate, 20 mM sodium cacodylate trihydrate, 40 mM bis-tris propane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.26→41.91 Å / Num. obs: 17196 / % possible obs: 91.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 41.35 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1587 / Rpim(I) all: 0.0948 / Rrim(I) all: 0.1858 / Net I/σ(I): 6.67
Reflection shellResolution: 2.26→2.341 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.442 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 1739 / CC1/2: 0.398 / CC star: 0.755 / Rpim(I) all: 0.8499 / Rrim(I) all: 1.683 / % possible all: 93.53

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4hr0

4hr0


Resolution: 2.26→41.91 Å / SU ML: 0.3396 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.3506
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 859 5 %
Rwork0.2016 16324 -
obs0.2034 17183 91.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.27 Å2
Refinement stepCycle: LAST / Resolution: 2.26→41.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2287 0 2 53 2342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00322338
X-RAY DIFFRACTIONf_angle_d0.54123168
X-RAY DIFFRACTIONf_chiral_restr0.0391354
X-RAY DIFFRACTIONf_plane_restr0.006404
X-RAY DIFFRACTIONf_dihedral_angle_d11.2877873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.40.33061440.27542740X-RAY DIFFRACTION93.3
2.4-2.590.31771440.26812725X-RAY DIFFRACTION92.97
2.59-2.850.30581430.24952719X-RAY DIFFRACTION92.32
2.85-3.260.27621410.22442704X-RAY DIFFRACTION92.07
3.26-4.10.20711430.17652701X-RAY DIFFRACTION90.86
4.11-41.910.20251440.16952735X-RAY DIFFRACTION89.52

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