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- PDB-4k6e: Crystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain i... -

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Basic information

Entry
Database: PDB / ID: 4k6e
TitleCrystal structure of Saccharomyces cerevisiae Dcp2 Nudix domain in complex with Mg
ComponentsmRNA-decapping enzyme subunit 2
KeywordsHYDROLASE / Nudix / mRNA decapping / Nudix hydrolase
Function / homology
Function and homology information


RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...RNA decapping complex / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / deadenylation-independent decapping of nuclear-transcribed mRNA / mRNA decay by 5' to 3' exoribonuclease / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / cytoplasmic side of membrane / deadenylation-dependent decapping of nuclear-transcribed mRNA / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of transcription initiation by RNA polymerase II / stress granule assembly / P-body / mRNA processing / manganese ion binding / hydrolase activity / mRNA binding / chromatin binding / nucleus / cytoplasm
Similarity search - Function
mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain ...mRNA decapping protein 2, Box A domain / mRNA decapping protein 2, Box A domain superfamily / mRNA decapping enzyme 2 , NUDIX hydrolase domain / Dcp2, box A domain / Dcp2, box A domain / NUDIX hydrolase, conserved site / Nudix box signature. / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
m7GpppN-mRNA hydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsAglietti, R.A. / Floor, S.N. / Gross, J.D.
CitationJournal: Structure / Year: 2013
Title: Active site conformational dynamics are coupled to catalysis in the mRNA decapping enzyme dcp2.
Authors: Aglietti, R.A. / Floor, S.N. / McClendon, C.L. / Jacobson, M.P. / Gross, J.D.
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_asym_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_asym_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_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: mRNA-decapping enzyme subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1452
Polymers17,1211
Non-polymers241
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.054, 85.054, 48.749
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

#1: Protein mRNA-decapping enzyme subunit 2 / Protein PSU1


Mass: 17120.549 Da / Num. of mol.: 1 / Fragment: Dcp2 Nudix domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: DCP2, N1917, PSU1, YNL118C / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P53550, Hydrolases
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 10 mM HEPES, 1 mM DTT, 50 mM NaCl, 100 mM Na2SO4, 0.1 M Mg Formate, 20% Peg 3350, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95372
DetectorDetector: CCD / Date: Apr 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 11889 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.081 / Χ2: 1.11 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.147.30.5575960.812199.7
2.14-2.187.40.5255890.8741100
2.18-2.227.30.3895860.839199.7
2.22-2.267.50.3725840.8741100
2.26-2.317.30.3415940.9021100
2.31-2.377.40.35830.973199.8
2.37-2.427.40.2695940.9461100
2.42-2.497.50.2235860.959199.8
2.49-2.567.30.2125870.9711100
2.56-2.657.40.1865920.944199.8
2.65-2.747.40.1595961.0111100
2.74-2.857.40.1265901.0761100
2.85-2.987.30.115851.1841100
2.98-3.147.30.0966001.4081100
3.14-3.337.30.0865911.5721100
3.33-3.597.20.0696001.8491100
3.59-3.957.20.0555961.6331100
3.95-4.5270.0386041.2051100
4.52-5.77.20.0336041.05199.8
5.7-507.10.0326321.1331100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→42.527 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8833 / SU ML: 0.18 / σ(F): 0 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1149 9.98 %random
Rwork0.153 ---
obs0.1568 11509 96.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.65 Å2 / Biso mean: 43.2572 Å2 / Biso min: 17.85 Å2
Refinement stepCycle: LAST / Resolution: 2.1→42.527 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1203 0 1 45 1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071227
X-RAY DIFFRACTIONf_angle_d1.0851647
X-RAY DIFFRACTIONf_chiral_restr0.079173
X-RAY DIFFRACTIONf_plane_restr0.004212
X-RAY DIFFRACTIONf_dihedral_angle_d14.385474
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.1960.22371380.18531234137292
2.196-2.31180.22451290.17141261139094
2.3118-2.45660.21651420.16761268141096
2.4566-2.64620.24211400.17011267140796
2.6462-2.91250.19751450.17661293143898
2.9125-3.33380.20521440.16941326147099
3.3338-4.19960.17821540.135613371491100
4.1996-42.53570.16021570.131513741531100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.9124-0.9638-0.52784.89870.97894.1553-0.0130.3036-0.066-0.0663-0.27040.3417-0.2474-0.29360.20540.22040.028-0.04440.2365-0.06440.228726.153119.635236.2532
25.27851.2081.47924.34580.5842.4371-0.0036-0.6623-0.72720.7527-0.16430.01560.7230.3097-0.07910.37130.04650.06140.24440.03860.256131.230112.470446.903
32.7701-0.16660.27063.38810.38262.79150.0219-0.2294-0.37170.4221-0.31190.89320.2505-0.51860.32440.3041-0.05930.09740.3668-0.09970.409721.827116.387546.1123
44.63440.52380.13155.63721.38043.9889-0.25370.0350.1594-0.4456-0.05110.2579-0.2613-0.06110.22680.17030.0339-0.00480.2034-0.0510.117326.365221.954242.1302
53.5951-0.32731.35142.9439-0.26654.86520.10650.44140.2439-0.4377-0.24540.131-0.4910.00360.17350.33790.0011-0.04090.2575-0.03170.150429.065123.265532.9713
65.4110.87840.61225.8556-2.33061.1028-0.05831.2656-0.0605-1.1391-0.32510.75180.2367-0.3769-0.35510.48090.0784-0.160.6702-0.24890.531519.921317.486426.676
72.1134-2.9202-3.92944.76645.16657.40060.24260.8614-0.37670.029-0.29880.59150.0603-0.0241-0.01770.31180.07690.00220.5573-0.13060.51499.958426.203243.0829
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 102:132 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 133:154 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 155:174 )A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 175:192 )A0
5X-RAY DIFFRACTION5CHAIN A AND (RESID 193:212 )A0
6X-RAY DIFFRACTION6CHAIN A AND (RESID 213:227 )A0
7X-RAY DIFFRACTION7CHAIN A AND (RESID 228:245 )A0

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