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- PDB-7otl: Structure of a psychrophilic CCA-adding enzyme crystallized by co... -

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Basic information

Entry
Database: PDB / ID: 7otl
TitleStructure of a psychrophilic CCA-adding enzyme crystallized by counter-diffusion
ComponentsCCA-adding enzyme
KeywordsRNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / psychrophilic enzyme
Function / homology
Function and homology information


tRNA processing / nucleotidyltransferase activity / tRNA binding / nucleotide binding
Similarity search - Function
CCA-adding enzyme, C-terminal / tRNA nucleotidyltransferase domain 2 putative / : / tRNA nucleotidyltransferase/poly(A) polymerase, RNA and SrmB- binding domain / Probable RNA and SrmB- binding site of polymerase A / Poly A polymerase, head domain / Poly A polymerase head domain / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Biological speciesPlanococcus halocryophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRollet, K. / de Wijn, R. / Hennig, O. / Betat, H. / Moerl, M. / Lorber, B. / Sauter, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-LABX-0036_NETRNA France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05 France
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: CCA-addition in the cold: Structural characterization of the psychrophilic CCA-adding enzyme from the permafrost bacterium Planococcus halocryophilus .
Authors: de Wijn, R. / Rollet, K. / Ernst, F.G.M. / Wellner, K. / Betat, H. / Morl, M. / Sauter, C.
History
DepositionJun 10, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
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: CCA-adding enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8835
Polymers48,4981
Non-polymers3844
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint-43 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.000, 70.000, 292.200
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

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Components

#1: Protein CCA-adding enzyme


Mass: 48498.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planococcus halocryophilus (bacteria) / Gene: BBI08_05760 / Plasmid: pET-30b(+) / Details (production host): pET-30bEk/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1C7DQ98
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.7 Å3/Da / Density % sol: 66.72 % / Description: bipyramid
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 5
Details: Protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; Crystals were obtained in capillaries filled with protein solution and sealed at one extremity and plunged in ...Details: Protein solution at 4.5 mg/mL in 50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; Crystals were obtained in capillaries filled with protein solution and sealed at one extremity and plunged in 3 M ammonium sulfate, 0.1 M sodium acetate pH 5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18615 / % possible obs: 98.6 % / Redundancy: 55.7 % / Biso Wilson estimate: 60.29 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.258 / Net I/σ(I): 21.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 57.5 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1819 / CC1/2: 1 / Rrim(I) all: 2.04 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QXN

6qxn


Resolution: 2.8→46.88 Å / SU ML: 0.3942 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.3979
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2578 901 4.84 %
Rwork0.2227 17701 -
obs0.2243 18602 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.31 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 20 20 3029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00883063
X-RAY DIFFRACTIONf_angle_d1.05344135
X-RAY DIFFRACTIONf_chiral_restr0.0615461
X-RAY DIFFRACTIONf_plane_restr0.0052517
X-RAY DIFFRACTIONf_dihedral_angle_d14.86921146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.980.37081580.28832873X-RAY DIFFRACTION99.97
2.98-3.210.34091560.27532929X-RAY DIFFRACTION100
3.21-3.530.25211480.24792946X-RAY DIFFRACTION100
3.53-4.040.28531200.25442708X-RAY DIFFRACTION91.26
4.04-5.090.18371660.16763017X-RAY DIFFRACTION99.97
5.09-46.880.26011530.20983228X-RAY DIFFRACTION99.85

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