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- PDB-4j7n: Crystal structure of mouse DXO in complex with M7GPPPG cap -

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Basic information

Entry
Database: PDB / ID: 4j7n
TitleCrystal structure of mouse DXO in complex with M7GPPPG cap
ComponentsProtein Dom3Z
KeywordsHYDROLASE / Decapping / 5'-3' exoribonuclease
Function / homology
Function and homology information


RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / NAD-cap decapping / nuclear mRNA surveillance / 5'-3' exonuclease activity / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters ...RNA NAD+-cap (NAD+-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / nucleic acid metabolic process / NAD-cap decapping / nuclear mRNA surveillance / 5'-3' exonuclease activity / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / nucleotide binding / mRNA binding / magnesium ion binding / nucleus
Similarity search - Function
RAI1-like / RAI1-like family / RAI1 like PD-(D/E)XK nuclease
Similarity search - Domain/homology
9-METHYLGUANINE / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / Decapping and exoribonuclease protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 1.5 Å
AuthorsKilic, T. / Chang, J.H. / Tong, L.
CitationJournal: Mol.Cell / Year: 2013
Title: A mammalian pre-mRNA 5' end capping quality control mechanism and an unexpected link of capping to pre-mRNA processing.
Authors: Jiao, X. / Chang, J.H. / Kilic, T. / Tong, L. / Kiledjian, M.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: Protein Dom3Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0296
Polymers43,1331
Non-polymers1,8965
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.910, 87.460, 53.270
Angle α, β, γ (deg.)90.00, 113.69, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein Dom3Z / Dom-3 homolog Z / DXO


Mass: 43132.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dom3z, Ng6 / Production host: Escherichia coli (E. coli) / References: UniProt: O70348
#2: Chemical ChemComp-GTG / 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / MRNA CAP ANALOG N7-METHYL GPPPG


Mass: 803.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N10O18P3
#3: Chemical ChemComp-9MG / 9-METHYLGUANINE


Mass: 165.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5O
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING 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 28, 2010 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 66690 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.7
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.9 / % possible all: 97.6

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Processing

Software
NameClassification
CBASSdata collection
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER / Resolution: 1.5→40.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 512189.2 / 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
Rfree0.2 3264 5.1 %RANDOM
Rwork0.172 ---
all0.18 ---
obs0.172 64292 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.0016 Å2 / ksol: 0.42 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20.94 Å2
2--0.24 Å20 Å2
3---0.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.5→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2889 0 124 442 3455
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.742.5
X-RAY DIFFRACTIONc_mcangle_it2.524
X-RAY DIFFRACTIONc_scbond_it3.223.5
X-RAY DIFFRACTIONc_scangle_it4.655
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.263 313 5.3 %
Rwork0.236 5550 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6gpppg.par

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