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- PDB-9du8: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -

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Basic information

Entry
Database: PDB / ID: 9du8
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP/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
ADENOSINE-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 (ADP/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)50,4378
Polymers49,4862
Non-polymers9526
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-93 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.375, 79.335, 91.822
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-MG / MAGNESIUM ION


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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.11 Å3/Da / Density % sol: 41.75 %
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 ADP and 5mM MgCl2, Puck: PSL-0201, 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 ADP and 5mM MgCl2, Puck: PSL-0201, 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→48.66 Å / Num. obs: 92588 / % possible obs: 99.9 % / Redundancy: 13 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Rrim(I) all: 0.056 / Χ2: 1.05 / Net I/σ(I): 23.4 / Num. measured all: 1201489
Reflection shellResolution: 1.35→1.37 Å / % possible obs: 98.5 % / Redundancy: 9.3 % / Rmerge(I) obs: 0.891 / Num. measured all: 41795 / Num. unique obs: 4471 / CC1/2: 0.826 / Rpim(I) all: 0.304 / Rrim(I) all: 0.943 / Χ2: 1.09 / Net I/σ(I) obs: 2.6

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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→48.66 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1687 4670 5.05 %
Rwork0.1429 --
obs0.1441 92500 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3224 0 58 372 3654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073512
X-RAY DIFFRACTIONf_angle_d1.1594796
X-RAY DIFFRACTIONf_dihedral_angle_d17.4581301
X-RAY DIFFRACTIONf_chiral_restr0.081524
X-RAY DIFFRACTIONf_plane_restr0.009615
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.23541480.19972832X-RAY DIFFRACTION98
1.37-1.380.23711450.18712896X-RAY DIFFRACTION100
1.38-1.40.23081430.17732927X-RAY DIFFRACTION100
1.4-1.420.20971760.15742842X-RAY DIFFRACTION100
1.42-1.430.19251500.14842919X-RAY DIFFRACTION100
1.43-1.450.19121460.14762886X-RAY DIFFRACTION100
1.45-1.480.19111380.14052916X-RAY DIFFRACTION100
1.48-1.50.16341470.13752911X-RAY DIFFRACTION100
1.5-1.520.18311600.13282888X-RAY DIFFRACTION100
1.52-1.550.17921730.13162891X-RAY DIFFRACTION100
1.55-1.570.16721460.12842902X-RAY DIFFRACTION100
1.57-1.60.19181580.13052912X-RAY DIFFRACTION100
1.6-1.630.17871640.12342882X-RAY DIFFRACTION100
1.63-1.660.16011800.12012910X-RAY DIFFRACTION100
1.66-1.70.14931380.11352913X-RAY DIFFRACTION100
1.7-1.740.15441500.11712940X-RAY DIFFRACTION100
1.74-1.780.15631710.12222891X-RAY DIFFRACTION100
1.78-1.830.16651490.13042921X-RAY DIFFRACTION100
1.83-1.890.16981230.13062953X-RAY DIFFRACTION100
1.89-1.950.15081750.13792897X-RAY DIFFRACTION100
1.95-2.020.1571440.13842931X-RAY DIFFRACTION100
2.02-2.10.17131690.13312929X-RAY DIFFRACTION100
2.1-2.190.15221620.1332931X-RAY DIFFRACTION100
2.19-2.310.17311750.13532925X-RAY DIFFRACTION100
2.31-2.450.16841530.14272956X-RAY DIFFRACTION100
2.45-2.640.161640.1392967X-RAY DIFFRACTION100
2.64-2.910.17951670.15522954X-RAY DIFFRACTION100
2.91-3.330.16991620.15382983X-RAY DIFFRACTION100
3.33-4.190.14951460.14273053X-RAY DIFFRACTION100
4.19-48.660.1791480.15843172X-RAY DIFFRACTION100

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