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- PDB-9etk: Crystal structure of Vibrio cholerae RNase AM -

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Basic information

Entry
Database: PDB / ID: 9etk
TitleCrystal structure of Vibrio cholerae RNase AM
ComponentsMetal-dependent phosphoesterases (PHP family)
KeywordsHYDROLASE / RNase / exoribonuclease
Function / homology: / PHP domain / PHP domain / Polymerase/histidinol phosphatase, N-terminal / DNA polymerase alpha chain like domain / Polymerase/histidinol phosphatase-like / catalytic activity / : / PHP domain-containing protein
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsLormand, J.D. / Sondermann, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI110740 United States
Citation
Journal: To Be Published
Title: Crystal Structure of Vibrio cholerase RNase AM
Authors: Lormand, J.D. / Sondermann, H.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Metal-dependent phosphoesterases (PHP family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,70013
Polymers32,7481
Non-polymers95212
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2150 Å2
ΔGint-115 kcal/mol
Surface area12710 Å2
Unit cell
Length a, b, c (Å)47.464, 163.919, 39.607
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Metal-dependent phosphoesterases (PHP family) / PHP domain-containing protein


Mass: 32747.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria)
Gene: D6U24_06320, ERS013186_00176, F0H40_05235, I7465_04955
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H5Y1H1

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Non-polymers , 5 types, 262 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 5
Details: 0.1 M Bis-Tris (pH 5.0), 0.2 M ammonium sulfate and 22.5 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03285 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 1, 2022
RadiationMonochromator: LN2 cooled double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03285 Å / Relative weight: 1
ReflectionResolution: 1.479→45.59 Å / Num. obs: 99127 / % possible obs: 99.32 % / Redundancy: 6.8 % / Biso Wilson estimate: 21.05 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 12.45
Reflection shellResolution: 1.48→1.5 Å / Redundancy: 4.4 % / Num. unique obs: 65 / CC1/2: 0.031 / CC star: 0.245 / % possible all: 91.43

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
pointlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→45.59 Å / SU ML: 0.2167 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.92
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.18 3776 3.81 %
Rwork0.1507 95271 -
obs0.1518 99047 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.61 Å2
Refinement stepCycle: LAST / Resolution: 1.48→45.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 52 250 2514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912371
X-RAY DIFFRACTIONf_angle_d0.88583233
X-RAY DIFFRACTIONf_chiral_restr0.0834341
X-RAY DIFFRACTIONf_plane_restr0.009422
X-RAY DIFFRACTIONf_dihedral_angle_d14.2542873
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.50.43511280.44213202X-RAY DIFFRACTION91.43
1.5-1.520.40611370.40033386X-RAY DIFFRACTION94.02
1.52-1.540.44281410.33473475X-RAY DIFFRACTION97.57
1.54-1.560.29731380.28123486X-RAY DIFFRACTION99.94
1.56-1.580.31671450.23753676X-RAY DIFFRACTION99.87
1.58-1.610.24861300.22373445X-RAY DIFFRACTION100
1.61-1.630.24121440.1893621X-RAY DIFFRACTION100
1.63-1.660.22981440.17863508X-RAY DIFFRACTION99.97
1.66-1.690.25061390.17043533X-RAY DIFFRACTION99.89
1.69-1.730.18741410.16393567X-RAY DIFFRACTION99.89
1.73-1.760.20971390.16813550X-RAY DIFFRACTION99.86
1.76-1.80.19411400.1633547X-RAY DIFFRACTION99.92
1.8-1.840.19681440.17213522X-RAY DIFFRACTION99.95
1.84-1.890.19781420.17693595X-RAY DIFFRACTION99.81
1.89-1.940.22811390.15153535X-RAY DIFFRACTION99.95
1.94-20.19381400.13313588X-RAY DIFFRACTION100
2-2.060.17051400.12393557X-RAY DIFFRACTION100
2.06-2.130.14711390.12323521X-RAY DIFFRACTION100
2.13-2.220.16111410.13113535X-RAY DIFFRACTION100
2.22-2.320.17821420.13973537X-RAY DIFFRACTION100
2.32-2.440.15831430.13143565X-RAY DIFFRACTION100
2.44-2.590.18691350.14253562X-RAY DIFFRACTION99.95
2.6-2.80.18091410.14443575X-RAY DIFFRACTION99.92
2.8-3.080.18051400.14813534X-RAY DIFFRACTION99.95
3.08-3.520.16121430.13693535X-RAY DIFFRACTION100
3.52-4.430.12451410.12463566X-RAY DIFFRACTION99.95
4.44-45.590.17751400.14843548X-RAY DIFFRACTION99.84

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