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- PDB-4qdv: Dcps in complex with covalent ligand -

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Basic information

Entry
Database: PDB / ID: 4qdv
TitleDcps in complex with covalent ligand
Componentsm7GpppX diphosphatase
KeywordsHYDROLASE / Decapping scavenger enzyme
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-30U / PHOSPHATE ION / m7GpppX diphosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.8 Å
AuthorsLiu, S.
CitationJournal: To be Published
Title: Dcps in complex with covalent ligands targeting Tyrosines
Authors: Liu, S.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 6, 2024Group: 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 / software / 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 / _software.name / _struct_conn.pdbx_leaving_atom_flag / _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: m7GpppX diphosphatase
B: m7GpppX diphosphatase
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,08917
Polymers154,3544
Non-polymers1,73513
Water0
1
A: m7GpppX diphosphatase
B: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0939
Polymers77,1772
Non-polymers9167
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10650 Å2
ΔGint-84 kcal/mol
Surface area25280 Å2
MethodPISA
2
C: m7GpppX diphosphatase
D: m7GpppX diphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9968
Polymers77,1772
Non-polymers8186
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10630 Å2
ΔGint-73 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.090, 105.510, 140.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
m7GpppX diphosphatase / / DCS-1 / Decapping scavenger enzyme / Hint-related 7meGMP-directed hydrolase / Histidine triad ...DCS-1 / Decapping scavenger enzyme / Hint-related 7meGMP-directed hydrolase / Histidine triad nucleotide-binding protein 5 / Histidine triad protein member 5 / HINT-5 / Scavenger mRNA-decapping enzyme DcpS


Mass: 38588.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCPS, DCS1, HINT5, HSPC015 / Production host: Escherichia coli (E. coli)
References: UniProt: Q96C86, 5'-(N7-methyl 5'-triphosphoguanosine)-[mRNA] diphosphatase
#2: Chemical ChemComp-30U / 4-{[(2,4-diaminoquinazolin-5-yl)oxy]methyl}benzenesulfonic acid


Mass: 346.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14N4O4S
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growMethod: vapor diffusion, hanging drop
Details: 22-25% PEG3350, 50 mM sodium chloride, 26% glycerol, crystals soaked in 1 mM compound overnight, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→84.26 Å / Num. obs: 35486 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 59.52 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 12
Reflection shellResolution: 2.8→3.13 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 4.1 / Num. unique all: 10201 / % possible all: 97.3

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Processing

Software
NameClassification
JDirectordata collection
BUSTERrefinement
autoPROCdata scaling
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.8→84.26 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.8961 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.37
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 1777 5.17 %RANDOM
Rwork0.2055 ---
obs0.2078 34391 91.53 %-
Displacement parametersBiso mean: 65.24 Å2
Baniso -1Baniso -2Baniso -3
1-8.4602 Å20 Å20 Å2
2--3.3709 Å20 Å2
3----11.8312 Å2
Refine analyzeLuzzati coordinate error obs: 0.395 Å
Refinement stepCycle: LAST / Resolution: 2.8→84.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9561 0 102 0 9663
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3482SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes269HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1465HARMONIC5
X-RAY DIFFRACTIONt_it9915HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1219SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10848SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9915HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg13470HARMONIC21.19
X-RAY DIFFRACTIONt_omega_torsion3.22
X-RAY DIFFRACTIONt_other_torsion21.61
LS refinement shellResolution: 2.8→2.89 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2997 147 5.05 %
Rwork0.2445 2766 -
all0.2473 2913 -
obs--91.53 %
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)
11.81710.10890.13991.0486-0.20650.6672-0.06210.3074-0.277-0.30260.0337-0.1497-0.00780.09480.0284-0.0211-0.01480.05350.0956-0.08020.266437.707235.53717.9342
21.0979-0.1270.45530.5384-0.37211.40030.084-0.0286-0.56980.01920.0464-0.06230.2960.0712-0.1304-0.06560.00830.0233-0.0256-0.08550.33943.918520.675530.8422
31.2253-0.0739-0.49860.614-0.15860.95230.05960.05940.4840.03240.066-0.1553-0.27670.1373-0.1256-0.0854-0.0382-0.0473-0.0254-0.05450.352994.522136.718237.7595
42.0049-0.7237-0.20841.70660.03640.5-0.1495-0.41640.47990.36890.2159-0.42330.0030.1413-0.0664-0.00710.0378-0.11670.1229-0.09620.258288.673421.74651.2721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A40 - 336
2X-RAY DIFFRACTION2{ B|* }B40 - 336
3X-RAY DIFFRACTION3{ C|* }C39 - 336
4X-RAY DIFFRACTION4{ D|* }D38 - 337

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