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- PDB-9dt7: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -

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Basic information

Entry
Database: PDB / ID: 9dt7
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (5-O-phosphono-alpha-D-ribofuranose 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
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
5-O-phosphono-alpha-D-ribofuranose / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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 (5-O-phosphono-alpha-D-ribofuranose bound)
Authors: Liu, L. / Lovell, S. / Buchko, G.W. / Battaile, K.P.
History
DepositionSep 30, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 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)49,9956
Polymers49,4862
Non-polymers5094
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8110 Å2
ΔGint-60 kcal/mol
Surface area16710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.509, 79.740, 91.709
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.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-HSX / 5-O-phosphono-alpha-D-ribofuranose / 5-O-phosphono-alpha-D-ribose / 5-O-phosphono-D-ribose / 5-O-phosphono-ribose


Type: D-saccharide, alpha linking / Mass: 230.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11O8P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Ribf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 42.11 %
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 8.4, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 CD/34. 5 hour soak in 2mM 5-O-phosphono-alpha-D-ribofuranose (HSX), Puck: PSL- ...Details: 25% (v/v) PEG 3350, 0.2M sodium acetate, 0.1 M Tris 8.4, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-107 CD/34. 5 hour soak in 2mM 5-O-phosphono-alpha-D-ribofuranose (HSX), Puck: PSL-1603, Cryo: 30% (v/v) PEG 3350, 0.2 M sodium acetate, 0.1 M Tris 8.4.

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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: Mar 24, 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: 1.15→91.71 Å / Num. obs: 127124 / % possible obs: 84.8 % / Redundancy: 10.9 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.014 / Rrim(I) all: 0.051 / Χ2: 1.03 / Net I/σ(I): 21.8 / Num. measured all: 1379941
Reflection shellResolution: 1.15→1.18 Å / % possible obs: 16.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.477 / Num. measured all: 3948 / Num. unique obs: 1749 / CC1/2: 0.773 / Rpim(I) all: 0.369 / Rrim(I) all: 0.609 / Χ2: 1.15 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.15→60.17 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1525 6266 4.93 %
Rwork0.1302 --
obs0.1313 127006 84.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→60.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 30 493 3739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013548
X-RAY DIFFRACTIONf_angle_d1.194864
X-RAY DIFFRACTIONf_dihedral_angle_d15.6681411
X-RAY DIFFRACTIONf_chiral_restr0.094546
X-RAY DIFFRACTIONf_plane_restr0.015637
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.15-1.160.3334180.3065433X-RAY DIFFRACTION9
1.16-1.180.2773430.2512967X-RAY DIFFRACTION20
1.18-1.190.2766750.21411496X-RAY DIFFRACTION32
1.19-1.210.20991100.20611965X-RAY DIFFRACTION42
1.21-1.220.23261510.19082469X-RAY DIFFRACTION53
1.22-1.240.20821600.16922935X-RAY DIFFRACTION63
1.24-1.260.20291730.16553323X-RAY DIFFRACTION71
1.26-1.280.18211890.153747X-RAY DIFFRACTION79
1.28-1.30.17222140.14044045X-RAY DIFFRACTION87
1.3-1.320.16732200.13184314X-RAY DIFFRACTION92
1.32-1.340.16592360.12734516X-RAY DIFFRACTION96
1.34-1.360.14632350.1224620X-RAY DIFFRACTION98
1.36-1.390.15222340.11934716X-RAY DIFFRACTION100
1.39-1.420.14962390.11674711X-RAY DIFFRACTION100
1.42-1.450.12492290.11534746X-RAY DIFFRACTION100
1.45-1.480.14612350.11324732X-RAY DIFFRACTION100
1.48-1.520.1622500.12074702X-RAY DIFFRACTION100
1.52-1.560.1472360.11144743X-RAY DIFFRACTION100
1.56-1.610.13412520.11244711X-RAY DIFFRACTION100
1.61-1.660.12792220.11514759X-RAY DIFFRACTION100
1.66-1.720.13362540.11534718X-RAY DIFFRACTION100
1.72-1.790.13352460.11544771X-RAY DIFFRACTION100
1.79-1.870.14772550.12434753X-RAY DIFFRACTION100
1.87-1.970.13322790.12274727X-RAY DIFFRACTION100
1.97-2.090.13712670.11944745X-RAY DIFFRACTION100
2.09-2.250.14452290.11644788X-RAY DIFFRACTION100
2.25-2.480.162610.12754808X-RAY DIFFRACTION100
2.48-2.840.16572330.13574851X-RAY DIFFRACTION100
2.84-3.570.15422590.13614857X-RAY DIFFRACTION100
3.57-60.170.15642620.14355072X-RAY DIFFRACTION100

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