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- PDB-9du9: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -

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Basic information

Entry
Database: PDB / ID: 9du9
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (GDP/Mg bound)
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / ADP-ribose diphosphatase
Function / homology
Function and homology information


ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / nucleotide binding / metal ion binding / cytosol
Similarity search - Function
Nucleoside diphosphate pyrophosphatase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (GDP/Mg bound)
Authors: Mian, M.R. / Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.
History
DepositionOct 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribose pyrophosphatase
B: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4698
Polymers49,4862
Non-polymers9846
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-91 kcal/mol
Surface area16190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.437, 79.552, 91.796
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ADP-ribose pyrophosphatase / ADP-ribose diphosphatase / ADP-ribose phosphohydrolase / Adenosine diphosphoribose pyrophosphatase


Mass: 24742.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPHS_45750 / Plasmid: KlpnC.20447.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GVQ7, ADP-ribose diphosphatase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.12 Å3/Da / Density % sol: 41.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.5, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 AB/12. 5 hour soak in 5mM GDP and 5mM MgCl2, Puck: PSL-0209, Cryo: 30% (v/v) ...Details: 25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.5, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 AB/12. 5 hour soak in 5mM GDP and 5mM MgCl2, Puck: PSL-0209, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.35→48.69 Å / Num. obs: 89405 / % possible obs: 96.4 % / Redundancy: 13.6 % / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.016 / Rrim(I) all: 0.059 / Χ2: 1.02 / Net I/σ(I): 26.5 / Num. measured all: 1212900
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 79.2 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.834 / Num. measured all: 43472 / Num. unique obs: 3693 / CC1/2: 0.73 / Rpim(I) all: 0.246 / Rrim(I) all: 0.872 / Χ2: 0.99 / Net I/σ(I) obs: 3.3

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Processing

Software
NameVersionClassification
PHENIX(dev_5449: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→48.69 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1871 4416 4.95 %
Rwork0.1566 --
obs0.1581 89271 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 60 344 3638
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053518
X-RAY DIFFRACTIONf_angle_d0.874805
X-RAY DIFFRACTIONf_dihedral_angle_d15.7721304
X-RAY DIFFRACTIONf_chiral_restr0.079524
X-RAY DIFFRACTIONf_plane_restr0.007614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.2881110.23192214X-RAY DIFFRACTION76
1.37-1.380.24391420.22212503X-RAY DIFFRACTION87
1.38-1.40.24651490.20142677X-RAY DIFFRACTION91
1.4-1.420.22571530.18662679X-RAY DIFFRACTION94
1.42-1.430.21661650.18092749X-RAY DIFFRACTION95
1.43-1.450.20271360.16582772X-RAY DIFFRACTION96
1.45-1.480.21291410.15942819X-RAY DIFFRACTION96
1.48-1.50.20071290.14962777X-RAY DIFFRACTION96
1.5-1.520.17691420.14392827X-RAY DIFFRACTION96
1.52-1.550.2021520.14592804X-RAY DIFFRACTION96
1.55-1.570.19571420.14752819X-RAY DIFFRACTION97
1.57-1.60.18391370.15882865X-RAY DIFFRACTION96
1.6-1.630.21231380.1472810X-RAY DIFFRACTION97
1.63-1.660.19581600.15152831X-RAY DIFFRACTION97
1.66-1.70.16811440.1392847X-RAY DIFFRACTION97
1.7-1.740.19611420.14072860X-RAY DIFFRACTION97
1.74-1.780.18621660.14442815X-RAY DIFFRACTION97
1.78-1.830.20281600.14292836X-RAY DIFFRACTION98
1.83-1.890.1841450.14262871X-RAY DIFFRACTION98
1.89-1.950.17771330.15012891X-RAY DIFFRACTION98
1.95-2.020.18281440.15362884X-RAY DIFFRACTION98
2.02-2.10.19011730.13732884X-RAY DIFFRACTION98
2.1-2.190.15751590.1392887X-RAY DIFFRACTION99
2.19-2.310.17081380.14852930X-RAY DIFFRACTION99
2.31-2.450.18161550.1582938X-RAY DIFFRACTION99
2.45-2.640.20421470.16452960X-RAY DIFFRACTION99
2.64-2.910.20941450.17652942X-RAY DIFFRACTION99
2.91-3.330.17261620.17252984X-RAY DIFFRACTION99
3.33-4.190.17911730.15013018X-RAY DIFFRACTION99
4.19-48.690.17211330.15453162X-RAY DIFFRACTION99

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