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- PDB-6d1q: Crystal structure of E. coli RppH-DapF complex, monomer -

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Basic information

Entry
Database: PDB / ID: 6d1q
TitleCrystal structure of E. coli RppH-DapF complex, monomer
Components
  • Diaminopimelate epimerase
  • RNA pyrophosphohydrolase
Keywordsisomerase/hydrolase / RNA decay / RppH / DapF / isomerase-hydrolase complex
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / pyrophosphatase activity / NAD-cap decapping / mRNA 5'-diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ...diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / RNA destabilization / pyrophosphatase activity / NAD-cap decapping / mRNA 5'-diphosphatase activity / deadenylation-dependent decapping of nuclear-transcribed mRNA / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / lysine biosynthetic process via diaminopimelate / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme activator activity / P-body / magnesium ion binding / protein homodimerization activity / cytoplasm / cytosol
Similarity search - Function
RNA pyrophosphohydrolase RppH / Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. ...RNA pyrophosphohydrolase RppH / Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / NUDIX hydrolase / 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 / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Diaminopimelate epimerase / RNA pyrophosphohydrolase / Diaminopimelate epimerase / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsGao, A. / Serganov, A.
Funding support United States, 11items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41 GM103403 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)S10 RR029205 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
Department of Energy (DOE, United States)KP1605010 United States
Department of Energy (DOE, United States)KC0401040 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)P41GM111244 United States
Department of Energy (DOE, United States)DE-SC0012704 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM112940 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM035769 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01AI108889 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)F99CA212474 United States
CitationJournal: Nucleic Acids Res. / Year: 2018
Title: Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.
Authors: Gao, A. / Vasilyev, N. / Luciano, D.J. / Levenson-Palmer, R. / Richards, J. / Marsiglia, W.M. / Traaseth, N.J. / Belasco, J.G. / Serganov, A.
History
DepositionApr 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity_name_com ...citation / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity_name_com.name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diaminopimelate epimerase
B: RNA pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4475
Polymers49,2842
Non-polymers1633
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-28 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.440, 192.320, 50.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-934-

HOH

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Components

#1: Protein Diaminopimelate epimerase / DAP epimerase / PLP-independent amino acid racemase


Mass: 30332.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: dapF, b3809, JW5592 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A6K1, UniProt: B7MH73*PLUS, diaminopimelate epimerase
#2: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase / Ap5A pyrophosphatase


Mass: 18951.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A776, UniProt: B7MLH6*PLUS, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 4 Å3/Da / Density % sol: 69.24 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 30% (v/v) PEG400 and 0.1 M CHES, pH 9.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.15→123.65 Å / Num. obs: 43324 / % possible obs: 99.1 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.2
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 1.557

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D13

6d13


Resolution: 2.15→123.65 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7
RfactorNum. reflection% reflection
Rfree0.2337 2000 4.65 %
Rwork0.2125 --
obs0.2135 43008 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→123.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3435 0 8 73 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083525
X-RAY DIFFRACTIONf_angle_d1.0514772
X-RAY DIFFRACTIONf_dihedral_angle_d3.3342427
X-RAY DIFFRACTIONf_chiral_restr0.055510
X-RAY DIFFRACTIONf_plane_restr0.007628
LS refinement shellHighest resolution: 2.15 Å / Rfactor Rfree: 0.3632 / Rfactor Rwork: 0.332

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