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- PDB-6d13: Crystal structure of E.coli RppH-DapF complex -

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Basic information

Entry
Database: PDB / ID: 6d13
TitleCrystal structure of E.coli RppH-DapF complex
Components
  • Diaminopimelate epimerase
  • RNA pyrophosphohydrolase
Keywordsisomerase/hydrolase / RNA decay / DapF / RppH / isomerase-hydrolase complex
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / mRNA 5'-diphosphatase activity / lysine biosynthetic process via diaminopimelate / mRNA catabolic process / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / 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
IODIDE ION / Diaminopimelate epimerase / RNA pyrophosphohydrolase
Similarity search - Component
Biological speciesEscherichia coli O45:K1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.06 Å
AuthorsGao, A. / Serganov, A.
Funding support United States, 11items
OrganizationGrant numberCountry
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)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
Department of Energy (DOE, United States)DE-SC0012704 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
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 11, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)52,62015
Polymers51,2452
Non-polymers1,37513
Water1448
1
A: Diaminopimelate epimerase
B: RNA pyrophosphohydrolase
hetero molecules

A: Diaminopimelate epimerase
B: RNA pyrophosphohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,24030
Polymers102,4894
Non-polymers2,75126
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)85.810, 85.810, 177.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: dapF, ECS88_4235 / Production host: Escherichia coli (E. coli) / References: UniProt: B7MH73, diaminopimelate epimerase
#2: Protein RNA pyrophosphohydrolase / (Di)nucleoside polyphosphate hydrolase


Mass: 20911.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O45:K1 (strain S88 / ExPEC) (bacteria)
Strain: S88 / ExPEC / Gene: rppH, nudH, ECS88_3125 / Production host: Escherichia coli (E. coli)
References: UniProt: B7MLH6, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#3: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion
Details: 15% (v/v)PEG4,000, 0.1 M Tris-HCl, pH 8.0, and 0.2 M KI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.06→77.25 Å / Num. obs: 13075 / % possible obs: 98.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 13.9
Reflection shellResolution: 3.06→3.27 Å / Rmerge(I) obs: 1.076 / Num. unique obs: 2296

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IJZ

4ijz


Resolution: 3.06→19.991 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.73
RfactorNum. reflection% reflection
Rfree0.2642 636 4.92 %
Rwork0.1866 --
obs0.1903 12933 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.06→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 14 8 3462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093521
X-RAY DIFFRACTIONf_angle_d1.0744765
X-RAY DIFFRACTIONf_dihedral_angle_d3.3092096
X-RAY DIFFRACTIONf_chiral_restr0.059506
X-RAY DIFFRACTIONf_plane_restr0.007627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0602-3.29550.34321370.26162366X-RAY DIFFRACTION98
3.2955-3.62540.3141160.22752431X-RAY DIFFRACTION100
3.6254-4.14590.26091350.17372439X-RAY DIFFRACTION100
4.1459-5.20810.23131140.15192475X-RAY DIFFRACTION99
5.2081-19.99110.25671340.19472586X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 37.484 Å / Origin y: 46.4308 Å / Origin z: 65.8566 Å
111213212223313233
T0.4985 Å2-0.0099 Å2-0.0272 Å2-0.7542 Å20.0163 Å2--0.4843 Å2
L2.2176 °2-0.6436 °2-0.6667 °2-2.1086 °20.4029 °2--1.4001 °2
S-0.0742 Å °-0.7097 Å °-0.2633 Å °0.2021 Å °0.067 Å °-0.1223 Å °0.1092 Å °0.1968 Å °0.0293 Å °
Refinement TLS groupSelection details: all

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