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- PDB-3bl9: Synthetic Gene Encoded DcpS bound to inhibitor DG157493 -

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Basic information

Entry
Database: PDB / ID: 3bl9
TitleSynthetic Gene Encoded DcpS bound to inhibitor DG157493
ComponentsScavenger mRNA-decapping enzyme DcpS
KeywordsHYDROLASE / MRNA DECAPPING ENZYME / DCPS / LIGAND COMPLEX / Cytoplasm / Nonsense-mediated mRNA decay / Nucleus / Polymorphism / Structural Genomics / PSI-2 / Protein Structure Initiative / Accelerated Technologies Center for Gene to 3D Structure / ATCG3D
Function / homology
Function and homology information


mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...mRNA methylguanosine-cap decapping / 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase / 5'-(N(7)-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase activity / mRNA decay by 3' to 5' exoribonuclease / RNA exonuclease activity / : / deadenylation-dependent decapping of nuclear-transcribed mRNA / RNA 7-methylguanosine cap binding / mRNA cis splicing, via spliceosome / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / P-body / mitochondrion / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like ...mRNA decapping enzyme DcpS N-terminal fold / mRNA decapping enzyme DcpS N-terminal domain / Scavenger mRNA decapping enzyme, N-terminal domain / Scavenger mRNA decapping enzyme DcpS/DCS2 / Scavenger mRNA decapping enzyme, N-terminal / Scavenger mRNA decapping enzyme (DcpS) N-terminal / Scavenger mRNA decapping enzyme C-term binding / Histidine triad, conserved site / HIT domain signature. / HIT-like / HIT family, subunit A / HIT-like superfamily / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DD2 / m7GpppX diphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsStaker, B.L. / Christensen, J. / Stewart, L. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: Acs Chem.Biol. / Year: 2008
Title: DcpS as a therapeutic target for spinal muscular atrophy.
Authors: Singh, J. / Salcius, M. / Liu, S.W. / Staker, B.L. / Mishra, R. / Thurmond, J. / Michaud, G. / Mattoon, D.R. / Printen, J. / Christensen, J. / Bjornsson, J.M. / Pollok, B.A. / Kiledjian, M. ...Authors: Singh, J. / Salcius, M. / Liu, S.W. / Staker, B.L. / Mishra, R. / Thurmond, J. / Michaud, G. / Mattoon, D.R. / Printen, J. / Christensen, J. / Bjornsson, J.M. / Pollok, B.A. / Kiledjian, M. / Stewart, L. / Jarecki, J. / Gurney, M.E.
History
DepositionDec 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Aug 30, 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Scavenger mRNA-decapping enzyme DcpS
B: Scavenger mRNA-decapping enzyme DcpS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2163
Polymers69,7832
Non-polymers4321
Water10,034557
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.406, 56.867, 59.504
Angle α, β, γ (deg.)62.350, 77.930, 79.540
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Scavenger mRNA-decapping enzyme DcpS / DCS-1 / Hint- related 7meGMP-directed hydrolase / Histidine triad protein member 5 / HINT-5


Mass: 34891.613 Da / Num. of mol.: 2 / Fragment: UNP residues 38-337
Source method: isolated from a genetically manipulated source
Details: SMT3 FUSION PROTEIN / Source: (gene. exp.) Homo sapiens (human) / Gene: DCPS, DCS1, HINT5 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96C86, Hydrolases
#2: Chemical ChemComp-DD2 / 5-{[1-(2,3-dichlorobenzyl)piperidin-4-yl]methoxy}quinazoline-2,4-diamine


Mass: 432.346 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H23Cl2N5O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.2 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Ammonium Formate, vapor diffusion, hanging drop, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 26, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 20.8 / Number: 220144 / Rmerge(I) obs: 0.052 / Χ2: 2.4 / D res high: 1.8 Å / D res low: 50 Å / Num. obs: 47420 / % possible obs: 91.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.885098.610.0323.0185.9
3.083.8897.310.0442.7135.9
2.693.0896.110.0652.6755.9
2.442.6995.110.0782.3725.6
2.272.4494.310.0892.1835.3
2.132.2793.410.1062.1675.2
2.032.1392.510.1321.9784.9
1.942.038810.1551.7683.3
1.861.9482.910.171.4521.8
1.81.8677.510.231.4061.5
ReflectionResolution: 1.8→50 Å / Num. obs: 47420 / % possible obs: 91.6 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.052 / Χ2: 2.397 / Net I/σ(I): 20.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.8-1.861.50.2340291.40677.5
1.86-1.941.80.1742641.45282.9
1.94-2.033.30.15545881.76888
2.03-2.134.90.13247881.97892.5
2.13-2.275.20.10648312.16793.4
2.27-2.445.30.08948732.18394.3
2.44-2.695.60.07849182.37295.1
2.69-3.085.90.06549902.67596.1
3.08-3.885.90.04450332.71397.3
3.88-505.90.03251063.01898.6

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT3.004data extraction
d*TREKdata scaling
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ST0

1st0


Resolution: 1.8→33.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.217 / WRfactor Rwork: 0.171 / SU B: 2.796 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2418 5.1 %RANDOM
Rwork0.174 ---
obs0.176 47411 91.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20.36 Å20.07 Å2
2---0.13 Å20.2 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4755 0 29 557 5341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224899
X-RAY DIFFRACTIONr_bond_other_d0.0020.023383
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9746650
X-RAY DIFFRACTIONr_angle_other_deg0.91838204
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2415571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.98323.541257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14415852
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8711543
X-RAY DIFFRACTIONr_chiral_restr0.0810.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021015
X-RAY DIFFRACTIONr_nbd_refined0.2110.2937
X-RAY DIFFRACTIONr_nbd_other0.2040.23647
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22283
X-RAY DIFFRACTIONr_nbtor_other0.0840.22554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2420
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.220.275
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.236
X-RAY DIFFRACTIONr_mcbond_it1.0891.53768
X-RAY DIFFRACTIONr_mcbond_other0.1971.51138
X-RAY DIFFRACTIONr_mcangle_it1.23224676
X-RAY DIFFRACTIONr_scbond_it2.03532327
X-RAY DIFFRACTIONr_scangle_it2.9564.51974
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8470.2881540.212811384877.053
1.847-1.8970.2061570.1962873376780.435
1.897-1.9520.2461540.1922883359884.408
1.952-2.0120.2471600.1852924352087.614
2.012-2.0780.2591740.1782957340791.899
2.078-2.1510.2281590.1732940333093.063
2.151-2.2320.2181490.1712820317993.394
2.232-2.3230.2171550.172707305193.805
2.323-2.4260.2331410.1742634293694.516
2.426-2.5440.2371350.182529280994.838
2.544-2.6810.2381230.1792426267795.219
2.681-2.8440.2371270.1872329255896.013
2.844-3.0390.2531150.182142234396.329
3.039-3.2820.2051010.1752054222496.897
3.282-3.5940.194970.171896205097.22
3.594-4.0150.203870.1611715184397.775
4.015-4.6320.183700.1381506160498.254
4.632-5.6620.229690.1611294138298.625
5.662-7.9610.248570.215988105399.24
7.961-52.20.161340.16356560798.682

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