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- PDB-6vcm: Crystal structure of E.coli RppH-DapF in complex with GTP, Mg2+ and F- -

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Basic information

Entry
Database: PDB / ID: 6vcm
TitleCrystal structure of E.coli RppH-DapF in complex with GTP, Mg2+ and F-
Components
  • Diaminopimelate epimerase
  • RNA pyrophosphohydrolase
KeywordsRNA BINDING PROTEIN/ISOMERASE / RNA degradation / RNA BINDING PROTEIN / RNA binding protein-isomerase complex
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / RNA decapping / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / lysine biosynthetic process via diaminopimelate / tRNA processing ...diaminopimelate epimerase / diaminopimelate epimerase activity / RNA NAD-cap (NMN-forming) hydrolase activity / RNA destabilization / mRNA 5'-diphosphatase activity / RNA decapping / NAD-cap decapping / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / lysine biosynthetic process via diaminopimelate / tRNA processing / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / enzyme activator activity / 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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase ...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 / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FLUORIDE ION / GUANOSINE-5'-TRIPHOSPHATE / Diaminopimelate epimerase / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsGao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01GM112940 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Principles of RNA and nucleotide discrimination by the RNA processing enzyme RppH.
Authors: Gao, A. / Vasilyev, N. / Kaushik, A. / Duan, W. / Serganov, A.
History
DepositionDec 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: 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 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7959
Polymers49,1202
Non-polymers6757
Water1,31573
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)162.357, 192.948, 51.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-201-

CL

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 30154.422 Da / Num. of mol.: 1 / Mutation: R36A, Y268A
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 BL21(DE3) (bacteria) / References: UniProt: P0A6K1, diaminopimelate epimerase
#2: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase / Ap5A pyrophosphatase


Mass: 18965.773 Da / Num. of mol.: 1 / Mutation: Q159A, E160A
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 BL21(DE3) (bacteria)
References: UniProt: P0A776, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Non-polymers , 5 types, 80 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-F / FLUORIDE ION


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F / Feature type: SUBJECT OF INVESTIGATION
#7: 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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Details

Has ligand of interestY

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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: 4.06 Å3/Da / Density % sol: 69.74 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9.2 / Details: 30% (v/v) PEG400, 0.1 M CHES, pH 9.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 33797 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 50.03 Å2 / CC1/2: 0.994 / Net I/σ(I): 22.2
Reflection shellResolution: 2.35→2.4 Å / Num. unique obs: 2208 / CC1/2: 0.65

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Processing

Software
NameVersionClassification
PHENIX1.16_3546refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D1V

6d1v


Resolution: 2.35→29.9 Å / SU ML: 0.2553 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.2229
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2345 1999 5.92 %
Rwork0.2124 31787 -
obs0.2138 33786 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.22 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3423 0 38 73 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00343555
X-RAY DIFFRACTIONf_angle_d0.69014825
X-RAY DIFFRACTIONf_chiral_restr0.0465515
X-RAY DIFFRACTIONf_plane_restr0.0039630
X-RAY DIFFRACTIONf_dihedral_angle_d23.55751312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.32841370.28522166X-RAY DIFFRACTION97.88
2.41-2.480.27191410.26742253X-RAY DIFFRACTION99.83
2.48-2.550.28751410.25572242X-RAY DIFFRACTION99.79
2.55-2.630.27931410.2552238X-RAY DIFFRACTION99.96
2.63-2.730.28111420.24972254X-RAY DIFFRACTION99.92
2.73-2.840.28091440.24192285X-RAY DIFFRACTION99.96
2.84-2.960.2471400.23782228X-RAY DIFFRACTION99.96
2.96-3.120.31781420.24082249X-RAY DIFFRACTION99.83
3.12-3.320.25051430.23792278X-RAY DIFFRACTION100
3.32-3.570.2211420.2142266X-RAY DIFFRACTION100
3.57-3.930.2561450.2172298X-RAY DIFFRACTION100
3.93-4.50.18261440.1822282X-RAY DIFFRACTION99.79
4.5-5.660.22541460.18382336X-RAY DIFFRACTION99.92
5.66-29.90.19621510.19042412X-RAY DIFFRACTION99.15

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