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- PDB-6gbs: Crystal Structure of the C. themophilum Scavenger Decapping Enzym... -

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Basic information

Entry
Database: PDB / ID: 6gbs
TitleCrystal Structure of the C. themophilum Scavenger Decapping Enzyme DcpS apo form
ComponentsPutative mRNA decapping protein
KeywordsHYDROLASE / mRNA decapping / decapping enzyme / scavenger decapping enzyme
Function / homology
Function and homology information


deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity
Similarity search - Function
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 / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Putative mRNA decapping protein
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum DSM 1495 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.946 Å
AuthorsFuchs, A.-L. / Neu, A. / Sprangers, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Molecular basis of the selective processing of short mRNA substrates by the DcpS mRNA decapping enzyme.
Authors: Fuchs, A.L. / Wurm, J.P. / Neu, A. / Sprangers, R.
History
DepositionApr 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative mRNA decapping protein
B: Putative mRNA decapping protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,35315
Polymers79,5022
Non-polymers85113
Water4,630257
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12190 Å2
ΔGint8 kcal/mol
Surface area30670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.595, 69.719, 70.947
Angle α, β, γ (deg.)104.480, 101.390, 111.610
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 133 or resid 135...
21(chain B and (resid 1 through 92 or resid 96...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETTYRTYR(chain A and (resid 1 through 133 or resid 135...AA1 - 1333 - 135
12ASPASPGLYGLY(chain A and (resid 1 through 133 or resid 135...AA135 - 159137 - 161
13LYSLYSLYSLYS(chain A and (resid 1 through 133 or resid 135...AA161163
21METMETSERSER(chain B and (resid 1 through 92 or resid 96...BB1 - 923 - 94
22ASPASPTYRTYR(chain B and (resid 1 through 92 or resid 96...BB96 - 13398 - 135
23METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335
24METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335
25LYSLYSARGARG(chain B and (resid 1 through 92 or resid 96...BB161 - 225163 - 227
26LYSLYSLYSLYS(chain B and (resid 1 through 92 or resid 96...BB227229
27METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335
28METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335
29METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335
210METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335
211METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335
212METMETALAALA(chain B and (resid 1 through 92 or resid 96...BB1 - 3333 - 335

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Components

#1: Protein Putative mRNA decapping protein / Scavenger Decapping Enzyme


Mass: 39750.949 Da / Num. of mol.: 2 / Mutation: H258N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum DSM 1495 (fungus)
Gene: CTHT_0038110 / Plasmid: pRSFM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): CodonPlusRIL / References: UniProt: G0S8A3
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 200 mM Ammoniumacetate, 100 mM BisTRIS pH 5.5, 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0004 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0004 Å / Relative weight: 1
ReflectionResolution: 1.946→48.503 Å / Num. obs: 115497 / % possible obs: 96.3 % / Redundancy: 3.428 % / Biso Wilson estimate: 28.85 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.102 / Χ2: 0.993 / Net I/σ(I): 9.82
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.95-23.5450.7052.144540.7460.83495.8
2-2.063.5150.5712.6442990.8030.67795.5
2.06-2.123.4290.4833.1142140.8410.57696
2.12-2.183.2940.4023.7141040.8720.48495.8
2.18-2.253.2290.3334.2539570.9040.40396.5
2.25-2.333.5170.275.5138700.9390.32196.1
2.33-2.423.4860.2266.3737520.9570.26896.6
2.42-2.523.4450.1967.1236320.9620.23497.2
2.52-2.633.3580.1648.1834600.9680.19697.3
2.63-2.763.2710.1299.6433190.980.15697.4
2.76-2.913.6190.10812.0731800.9860.12797.9
2.91-3.083.5810.08614.2430030.9890.10298
3.08-3.33.4970.07115.7827890.9920.08497.4
3.3-3.563.2130.05717.7125980.9930.0796.9
3.56-3.93.5320.04921.5423790.9950.05995.9
3.9-4.363.4690.04523.0921250.9950.05395.5
4.36-5.033.2520.04423.3418740.9960.05394.6
5.03-6.173.380.04422.8315620.9950.05394.8
6.17-8.723.4120.04323.7112220.9930.05294.1
8.72-48.5033.3510.03826.575960.9960.04585.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.06 Å48.5 Å
Translation4.06 Å48.5 Å

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASER2.7.17phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BV3

5bv3


Resolution: 1.946→48.503 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 24.54 / Details: molecular replacement
RfactorNum. reflection% reflectionSelection details
Rfree0.2165 5768 5 %random
Rwork0.1828 ---
obs0.1845 115456 91.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 122.25 Å2 / Biso mean: 34.6344 Å2 / Biso min: 16.31 Å2
Refinement stepCycle: final / Resolution: 1.946→48.503 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5371 0 137 257 5765
Biso mean--64.24 34.95 -
Num. residues----663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075572
X-RAY DIFFRACTIONf_angle_d0.877535
X-RAY DIFFRACTIONf_chiral_restr0.054812
X-RAY DIFFRACTIONf_plane_restr0.005976
X-RAY DIFFRACTIONf_dihedral_angle_d18.8443345
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3144X-RAY DIFFRACTION9.785TORSIONAL
12B3144X-RAY DIFFRACTION9.785TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9456-1.96770.2981760.29063355353185
1.9677-1.99090.34021980.30223698389691
1.9909-2.01520.31111860.28763650383692
2.0152-2.04070.32441990.2853653385291
2.0407-2.06750.32061860.27673606379292
2.0675-2.09590.27541960.26683705390191
2.0959-2.12580.32061880.25833574376291
2.1258-2.15750.30671950.26113626382191
2.1575-2.19120.30541900.25373654384491
2.1912-2.22720.27741890.25263583377291
2.2272-2.26560.30591940.23773702389691
2.2656-2.30680.26571850.23373578376391
2.3068-2.35110.2751900.2233671386191
2.3511-2.39910.25061960.21623699389592
2.3991-2.45130.28831950.21373594378992
2.4513-2.50830.26851970.2183759395693
2.5083-2.5710.28991870.21313653384093
2.571-2.64050.25021930.20163739393293
2.6405-2.71820.21422010.19013707390893
2.7182-2.8060.22861950.18463794398995
2.806-2.90620.22092030.1823799400295
2.9062-3.02260.25611970.183757395495
3.0226-3.16010.22262000.17773771397195
3.1601-3.32670.2061990.17443777397694
3.3267-3.53510.23981950.16913723391893
3.5351-3.80790.17071900.14873640383091
3.8079-4.19090.1421890.12983585377490
4.1909-4.79690.12911920.11663575376789
4.7969-6.04180.16091820.14683528371089
6.0418-48.51840.16651850.14953533371888
Refinement TLS params.Method: refined / Origin x: 33.9249 Å / Origin y: 36.0339 Å / Origin z: 13.366 Å
111213212223313233
T0.2014 Å2-0.0339 Å2-0.0105 Å2-0.1992 Å20.0199 Å2--0.205 Å2
L0.4386 °2-0.0243 °2-0.1198 °2-0.2989 °20.1109 °2--0.349 °2
S0.0102 Å °-0.0401 Å °-0.0041 Å °-0.0011 Å °-0.0197 Å °0.0206 Å °0.021 Å °0.0193 Å °0.0101 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 333
2X-RAY DIFFRACTION1allB1 - 333
3X-RAY DIFFRACTION1allD1 - 106
4X-RAY DIFFRACTION1allD107 - 326
5X-RAY DIFFRACTION1allD327 - 362
6X-RAY DIFFRACTION1allC2 - 10
7X-RAY DIFFRACTION1allC11 - 14
8X-RAY DIFFRACTION1allC15
9X-RAY DIFFRACTION1allE1

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