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- PDB-6d1v: Crystal structure of E. coli RppH-DapF complex, monomer bound to RNA -

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Basic information

Entry
Database: PDB / ID: 6d1v
TitleCrystal structure of E. coli RppH-DapF complex, monomer bound to RNA
Components
  • Diaminopimelate epimerase
  • RNA (5'-D(*(APC))-R(P*GP*U)-3')
  • RNA pyrophosphohydrolase
Keywordsisomerase/hydrolase/rna / RNA decay / RppH / DapF / isomerase-hydrolase complex / isomerase-hydrolase-rna complex
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / mRNA 5'-diphosphatase activity / RNA destabilization / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / tRNA processing / lysine biosynthetic process via diaminopimelate ...diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA decapping / mRNA 5'-diphosphatase activity / RNA destabilization / NAD-cap decapping / 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 / magnesium ion binding / protein homodimerization activity / cytosol / cytoplasm
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
RNA / RNA pyrophosphohydrolase / Diaminopimelate epimerase / Diaminopimelate epimerase / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.81 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.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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_conn_type
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_asym_id / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diaminopimelate epimerase
B: RNA pyrophosphohydrolase
C: RNA (5'-D(*(APC))-R(P*GP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,21618
Polymers50,3213
Non-polymers89515
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)160.644, 191.986, 51.207
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-207-

CL

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Diaminopimelate epimerase /


Mass: 30332.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: dapF / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6K1, UniProt: A7ZU14*PLUS
#2: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase / Ap5A pyrophosphatase


Mass: 18894.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rppH, nudH, ygdP, b2830, JW2798 / Production host: Escherichia coli (E. coli)
References: UniProt: P0A776, UniProt: A7ZQT6*PLUS, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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RNA chain , 1 types, 1 molecules C

#3: RNA chain RNA (5'-D(*(APC))-R(P*GP*U)-3')


Mass: 1093.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli)

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Non-polymers , 4 types, 303 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 288 / 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: 3.92 Å3/Da / Density % sol: 68.65 %
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: 1.81→123.2 Å / Num. obs: 70344 / % possible obs: 96.8 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 12.6
Reflection shellResolution: 1.81→1.85 Å / Rmerge(I) obs: 0.989 / Num. unique all: 3453

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementResolution: 1.81→61.601 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1
RfactorNum. reflection% reflection
Rfree0.2196 2000 2.84 %
Rwork0.1988 --
obs0.1994 70302 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.81→61.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 58 49 289 3834
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083630
X-RAY DIFFRACTIONf_angle_d1.0364918
X-RAY DIFFRACTIONf_dihedral_angle_d5.8382970
X-RAY DIFFRACTIONf_chiral_restr0.058520
X-RAY DIFFRACTIONf_plane_restr0.006633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8104-1.85560.36931210.33994139X-RAY DIFFRACTION83
1.8556-1.90580.36241450.3154977X-RAY DIFFRACTION99
1.9058-1.96190.33151460.28154931X-RAY DIFFRACTION99
1.9619-2.02520.27671440.25654936X-RAY DIFFRACTION99
2.0252-2.09760.25541440.24964942X-RAY DIFFRACTION99
2.0976-2.18160.26741450.22974945X-RAY DIFFRACTION99
2.1816-2.28090.24981450.22284963X-RAY DIFFRACTION99
2.2809-2.40110.29341450.22694926X-RAY DIFFRACTION99
2.4011-2.55160.26891460.21674989X-RAY DIFFRACTION99
2.5516-2.74860.26491430.22154877X-RAY DIFFRACTION97
2.7486-3.02520.21641440.20974915X-RAY DIFFRACTION98
3.0252-3.46290.23141420.19954872X-RAY DIFFRACTION96
3.4629-4.36270.18091420.16764865X-RAY DIFFRACTION95
4.3627-61.63710.1711480.16615025X-RAY DIFFRACTION94

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