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- PDB-9b22: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -

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Basic information

Entry
Database: PDB / ID: 9b22
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (ADP Ribose and AMP 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-ribose diphosphatase / ADP-ribose diphosphatase activity / metal ion binding
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 MONOPHOSPHATE / Chem-AR6 / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 Ribose and AMP bound)
Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.
History
DepositionMar 14, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,0499
Polymers49,4862
Non-polymers1,5637
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-78 kcal/mol
Surface area16060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.826, 92.659, 57.716
Angle α, β, γ (deg.)90.00, 91.68, 90.00
Int Tables number4
Space group name H-MP1211

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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-AR6 / [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H2O
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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 23% PEG 4000, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. 3 minutue soak in 15 mM AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D- ...Details: 23% PEG 4000, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. 3 minutue soak in 15 mM AMP and 15 mM ADP-ribose. Electron density consistent with the alpha-D-ribose form. Subunit B contains AMP and ADP-ribose in the active site and were refined with grouped occupancies. plate Liu-S-102, F8. Puck: PSL-1011, Cryo: 10% extra PEG 4000 added to the drop.

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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: Feb 10, 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: 1.3→36.58 Å / Num. obs: 100227 / % possible obs: 97.7 % / Redundancy: 6.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.023 / Rrim(I) all: 0.061 / Χ2: 0.95 / Net I/σ(I): 14.3 / Num. measured all: 641274
Reflection shellResolution: 1.3→1.33 Å / % possible obs: 80 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.692 / Num. measured all: 25108 / Num. unique obs: 6043 / CC1/2: 0.695 / Rpim(I) all: 0.377 / Rrim(I) all: 0.793 / Χ2: 0.9 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(dev_5243: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→36.58 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1635 4954 4.95 %
Rwork0.1365 --
obs0.1378 100180 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 99 376 3704
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073535
X-RAY DIFFRACTIONf_angle_d1.0194827
X-RAY DIFFRACTIONf_dihedral_angle_d18.7511388
X-RAY DIFFRACTIONf_chiral_restr0.078535
X-RAY DIFFRACTIONf_plane_restr0.011622
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.26591250.24162471X-RAY DIFFRACTION75
1.31-1.330.27981170.23032691X-RAY DIFFRACTION83
1.33-1.350.2551350.21092842X-RAY DIFFRACTION88
1.35-1.360.24171730.19412989X-RAY DIFFRACTION93
1.36-1.380.1981780.1833106X-RAY DIFFRACTION96
1.38-1.40.23571820.17413150X-RAY DIFFRACTION99
1.4-1.420.20621540.17253268X-RAY DIFFRACTION99
1.42-1.440.20191760.16723232X-RAY DIFFRACTION100
1.44-1.460.21521700.1573218X-RAY DIFFRACTION100
1.46-1.490.19361590.15213226X-RAY DIFFRACTION100
1.49-1.510.1891830.14023267X-RAY DIFFRACTION100
1.51-1.540.20661760.13733235X-RAY DIFFRACTION100
1.54-1.570.17291900.12883206X-RAY DIFFRACTION100
1.57-1.60.14761660.12393274X-RAY DIFFRACTION100
1.6-1.640.15611800.11783168X-RAY DIFFRACTION100
1.64-1.680.18111740.1183265X-RAY DIFFRACTION100
1.68-1.720.14921930.1163234X-RAY DIFFRACTION100
1.72-1.760.15931490.11913238X-RAY DIFFRACTION100
1.76-1.820.16681910.12353256X-RAY DIFFRACTION100
1.82-1.870.16861730.12713212X-RAY DIFFRACTION100
1.87-1.940.16961840.12623237X-RAY DIFFRACTION100
1.94-2.020.14151570.12333253X-RAY DIFFRACTION100
2.02-2.110.15971680.1233258X-RAY DIFFRACTION100
2.11-2.220.16541660.12583271X-RAY DIFFRACTION100
2.22-2.360.16121620.12663255X-RAY DIFFRACTION100
2.36-2.540.15871460.13093254X-RAY DIFFRACTION100
2.54-2.80.1321400.1333291X-RAY DIFFRACTION100
2.8-3.210.17261560.14543268X-RAY DIFFRACTION99
3.21-4.040.14971650.13443270X-RAY DIFFRACTION100
4.04-36.580.14771660.14343321X-RAY DIFFRACTION100

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