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- PDB-4gpu: Crystal structure of K. lactis Dxo1 (YDR370C) in complex with man... -

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Basic information

Entry
Database: PDB / ID: 4gpu
TitleCrystal structure of K. lactis Dxo1 (YDR370C) in complex with manganese
ComponentsKLLA0E02245p
KeywordsHYDROLASE / Decapping / 5'-3' exoribonuclease
Function / homology
Function and homology information


RNA NAD+-cap (NAD+-forming) hydrolase activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / RNA binding ...RNA NAD+-cap (NAD+-forming) hydrolase activity / mRNA 5'-diphosphatase activity / NAD-cap decapping / nucleic acid metabolic process / nuclear mRNA surveillance / 5'-3' exonuclease activity / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / RNA binding / nucleus / metal ion binding / cytosol
Similarity search - Function
RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease
Similarity search - Domain/homology
: / Decapping and exoribonuclease protein 1
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsChang, J.H. / Chiba, K. / Tong, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Dxo1 is a new type of eukaryotic enzyme with both decapping and 5'-3' exoribonuclease activity.
Authors: Chang, J.H. / Jiao, X. / Chiba, K. / Oh, C. / Martin, C.E. / Kiledjian, M. / Tong, L.
History
DepositionAug 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KLLA0E02245p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6012
Polymers48,5461
Non-polymers551
Water88349
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.130, 82.130, 260.730
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe authors have confirmed that the protein in monomeric by gel filtration analysis

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Components

#1: Protein KLLA0E02245p


Mass: 48546.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast)
Strain: ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37
Gene: KLLA0E02245g, KLLA0_E02245g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CPU0
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.61 Å3/Da / Density % sol: 52.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Sodium citrate tribasic, 23.5% (w/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. all: 13714 / Num. obs: 13599 / % possible obs: 99 % / Biso Wilson estimate: 27.4 Å2

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 4GPS

4gps


Resolution: 2.8→29.85 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 161829.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 659 5.1 %RANDOM
Rwork0.202 ---
obs0.202 12851 94.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.5487 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 78.4 Å2
Baniso -1Baniso -2Baniso -3
1-12.36 Å20 Å20 Å2
2--12.36 Å20 Å2
3----24.73 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 1 49 2741
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.431 48 4.3 %
Rwork0.334 1080 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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