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- PDB-6qxn: Crystal structure of the CCA-adding enzyme of a psychrophilic org... -

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Basic information

Entry
Database: PDB / ID: 6qxn
TitleCrystal structure of the CCA-adding enzyme of a psychrophilic organism in complex with CTP
ComponentsCCA-adding enzymeCCA tRNA nucleotidyltransferase
KeywordsRNA BINDING PROTEIN / tRNA maturation / tRNA nucleotidyltransferase / psychrophilic enzyme
Function / homology
Function and homology information


RNA 3'-end processing / tRNA processing / nucleotidyltransferase activity / nucleotide binding / RNA binding / metal ion binding
Similarity search - Function
Serum Albumin; Chain A, Domain 1 - #80 / 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 / Serum Albumin; Chain A, Domain 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 ...Serum Albumin; Chain A, Domain 1 - #80 / 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 / Serum Albumin; Chain A, Domain 1 / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / CYTIDINE-5'-TRIPHOSPHATE / PHOSPHATE ION / CCA-adding protein
Similarity search - Component
Biological speciesPlanococcus halocryophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 Å
Authorsde Wijn, R. / Rollet, K. / Bluhm, A. / 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 BiologyANR-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. / Wellner, K. / Betat, H. / Morl, M. / Sauter, C.
History
DepositionMar 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: CCA-adding enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4388
Polymers48,4981
Non-polymers9397
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-8 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.380, 70.380, 291.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CCA-adding enzyme / CCA tRNA nucleotidyltransferase


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, CCA tRNA nucleotidyltransferase

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Non-polymers , 5 types, 275 molecules

#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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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: 3.73 Å3/Da / Density % sol: 66.99 % / Description: bipyramid
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: protein solution at 4.5 mg/mL in50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate remarks : soaking 30 ...Details: protein solution at 4.5 mg/mL in50 mM Tris-HCl pH 7.5, 200 mM NaCl, 5 mM MgCl2; reservoir solution: 100 mM Sodium acetate; pH 4.5 1 M di-Ammonium hydrogen phosphate remarks : soaking 30 seconds in a drop with 5 mM CTP and reservoir solution + 18% glycerol
PH range: 4.5 - 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.849→50 Å / Num. obs: 63935 / % possible obs: 99.8 % / Redundancy: 12.2 % / Biso Wilson estimate: 40.9 Å2 / CC1/2: 1 / Rrim(I) all: 0.069 / Net I/σ(I): 22.11
Reflection shellResolution: 1.849→1.96 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 0.95 / Num. unique obs: 10060 / CC1/2: 0.451 / Rrim(I) all: 2.394 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDS20160617data reduction
XSCALE20160617data scaling
PHENIX1.13_2998phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MIV

1miv


Resolution: 1.849→49.056 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.52
RfactorNum. reflection% reflection
Rfree0.2187 3195 5 %
Rwork0.2019 --
obs0.2028 63868 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.849→49.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3072 0 58 268 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083186
X-RAY DIFFRACTIONf_angle_d0.9794301
X-RAY DIFFRACTIONf_dihedral_angle_d16.251200
X-RAY DIFFRACTIONf_chiral_restr0.06475
X-RAY DIFFRACTIONf_plane_restr0.006540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8488-1.87640.55141280.5582435X-RAY DIFFRACTION95
1.8764-1.90570.551360.53012593X-RAY DIFFRACTION100
1.9057-1.9370.411370.44042587X-RAY DIFFRACTION100
1.937-1.97040.37781360.38072591X-RAY DIFFRACTION100
1.9704-2.00620.35591370.32092612X-RAY DIFFRACTION100
2.0062-2.04480.35291370.28562589X-RAY DIFFRACTION100
2.0448-2.08650.26911370.2532603X-RAY DIFFRACTION100
2.0865-2.13190.25311370.23722609X-RAY DIFFRACTION100
2.1319-2.18150.27251370.23232595X-RAY DIFFRACTION100
2.1815-2.23610.25171370.23252600X-RAY DIFFRACTION100
2.2361-2.29650.2611380.22062622X-RAY DIFFRACTION100
2.2965-2.36410.25121380.2172634X-RAY DIFFRACTION100
2.3641-2.44040.24151390.20992615X-RAY DIFFRACTION100
2.4404-2.52760.22331380.20412636X-RAY DIFFRACTION100
2.5276-2.62880.21481380.20392632X-RAY DIFFRACTION100
2.6288-2.74840.22031390.20772634X-RAY DIFFRACTION100
2.7484-2.89330.23771390.20142640X-RAY DIFFRACTION100
2.8933-3.07460.26191400.21312657X-RAY DIFFRACTION100
3.0746-3.31190.21981410.20682684X-RAY DIFFRACTION100
3.3119-3.64510.21761410.19692690X-RAY DIFFRACTION100
3.6451-4.17230.17221440.16452721X-RAY DIFFRACTION100
4.1723-5.25570.15031450.14892756X-RAY DIFFRACTION100
5.2557-49.07360.19591560.18482938X-RAY DIFFRACTION100

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