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

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Basic information

Entry
Database: PDB / ID: 6vck
TitleCrystal structure of E.coli RppH-DapF in complex with GDP, 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 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
FLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / Diaminopimelate epimerase / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 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 / pdbx_struct_conn_angle / struct_conn
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.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)49,6918
Polymers49,1202
Non-polymers5716
Water1,838102
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)161.840, 193.601, 51.037
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-205-

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, 108 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-F / FLUORIDE ION / Fluoride


Mass: 18.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.9 Å3/Da / Density % sol: 68.47 %
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: 2.69→28.93 Å / Num. obs: 22647 / % possible obs: 99.43 % / Redundancy: 6.6 % / Biso Wilson estimate: 75.23 Å2 / CC1/2: 0.995 / Net I/σ(I): 24.56
Reflection shellResolution: 2.7→2.8 Å / Num. unique obs: 2203 / CC1/2: 0.698

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Processing

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

6d1v


Resolution: 2.69→28.93 Å / SU ML: 0.3832 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.684
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2682 1999 8.83 %
Rwork0.2264 20642 -
obs0.2301 22641 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.08 Å2
Refinement stepCycle: LAST / Resolution: 2.69→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3419 0 33 102 3554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473542
X-RAY DIFFRACTIONf_angle_d0.78314808
X-RAY DIFFRACTIONf_chiral_restr0.0505515
X-RAY DIFFRACTIONf_plane_restr0.0045629
X-RAY DIFFRACTIONf_dihedral_angle_d22.08831294
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.760.46421310.36461350X-RAY DIFFRACTION94.27
2.76-2.830.3161430.28861488X-RAY DIFFRACTION99.94
2.83-2.920.32461370.25981421X-RAY DIFFRACTION99.87
2.92-3.010.26491440.2591484X-RAY DIFFRACTION99.94
3.01-3.120.33331400.26291439X-RAY DIFFRACTION99.75
3.12-3.240.27721440.26111483X-RAY DIFFRACTION100
3.24-3.390.28651420.24671467X-RAY DIFFRACTION99.88
3.39-3.570.29281400.231448X-RAY DIFFRACTION100
3.57-3.790.27531430.24331478X-RAY DIFFRACTION99.63
3.79-4.090.24791430.21791475X-RAY DIFFRACTION99.94
4.09-4.50.23291450.18811496X-RAY DIFFRACTION99.94
4.5-5.140.21331450.18861498X-RAY DIFFRACTION99.88
5.14-6.470.29311480.22521523X-RAY DIFFRACTION99.94
6.47-28.930.271540.2291592X-RAY DIFFRACTION99.71

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