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- PDB-5bth: Crystal structure of Candida albicans Rai1 -

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Basic information

Entry
Database: PDB / ID: 5bth
TitleCrystal structure of Candida albicans Rai1
ComponentsDecapping nuclease RAI1
KeywordsHYDROLASE / Rai1 / Decapping / mRNA 5'-processing
Function / homology
Function and homology information


RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping ...RNA polymerase II termination complex / positive regulation of termination of RNA polymerase II transcription / RNA NAD+-cap (NAD+-forming) hydrolase activity / termination of RNA polymerase II transcription, poly(A)-coupled / Las1 complex / phosphodiesterase decapping endonuclease activity / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA 5'-diphosphatase activity / nuclear polyadenylation-dependent rRNA catabolic process / NAD-cap decapping / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / nuclear-transcribed mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme regulator activity / mRNA processing / nucleotide binding / RNA binding / metal ion binding / nucleus / cytosol
Similarity search - Function
RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease
Similarity search - Domain/homology
Decapping nuclease RAI1
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsWang, V.Y. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM090059 United States
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural and biochemical studies of the distinct activity profiles of Rai1 enzymes.
Authors: Wang, V.Y. / Jiao, X. / Kiledjian, M. / Tong, L.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Refinement description
Category: citation / pdbx_audit_support ...citation / pdbx_audit_support / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Decapping nuclease RAI1


Theoretical massNumber of molelcules
Total (without water)45,7461
Polymers45,7461
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.187, 98.793, 115.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Decapping nuclease RAI1


Mass: 45746.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: RAI1, CaO19.13610, CaO19.6230 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5AAT0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M Bis-Tris and 18% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 30, 2013
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 23150 / % possible obs: 97 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 27.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 6.2 / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.2→33.09 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 9.74 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.298 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29203 1237 5.1 %RANDOM
Rwork0.22921 ---
obs0.2323 23150 97.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.665 Å2
Baniso -1Baniso -2Baniso -3
1-8.97 Å20 Å2-0 Å2
2---3.12 Å20 Å2
3----5.85 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 0 78 3295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023280
X-RAY DIFFRACTIONr_bond_other_d0.0010.023159
X-RAY DIFFRACTIONr_angle_refined_deg1.7541.9714430
X-RAY DIFFRACTIONr_angle_other_deg0.83337301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3265390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.82425158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.68615631
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9791518
X-RAY DIFFRACTIONr_chiral_restr0.0940.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023647
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02729
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.318 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.397 176 -
Rwork0.399 3292 -
obs--95.25 %

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