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

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Basic information

Entry
Database: PDB / ID: 9dua
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (GMP 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'-MONOPHOSPHATE / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 (GMP bound)
Authors: 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)50,0945
Polymers49,3442
Non-polymers7513
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8530 Å2
ΔGint-54 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.545, 80.309, 91.667
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: 24671.770 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-5GP / GUANOSINE-5'-MONOPHOSPHATE


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 20% (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 5mM GMP, Puck: PSL-0801, Cryo: 30% (v/v) PEG 3350, 0.2 M ...Details: 20% (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 5mM GMP, Puck: PSL-0801, 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: 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: 1.4→91.67 Å / Num. obs: 81473 / % possible obs: 96.8 % / Redundancy: 12.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.021 / Rrim(I) all: 0.075 / Χ2: 1.01 / Net I/σ(I): 17.6 / Num. measured all: 1020007
Reflection shellResolution: 1.4→1.44 Å / % possible obs: 75 % / Redundancy: 7.8 % / Rmerge(I) obs: 1.151 / Num. measured all: 35427 / Num. unique obs: 4551 / CC1/2: 0.626 / Rpim(I) all: 0.428 / Rrim(I) all: 1.233 / Χ2: 0.99 / 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: 1.4→60.41 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1884 4105 5.04 %
Rwork0.1584 --
obs0.1599 81393 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4→60.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3218 0 49 375 3642
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063399
X-RAY DIFFRACTIONf_angle_d0.8534629
X-RAY DIFFRACTIONf_dihedral_angle_d13.2181273
X-RAY DIFFRACTIONf_chiral_restr0.075514
X-RAY DIFFRACTIONf_plane_restr0.009596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.2977980.2271948X-RAY DIFFRACTION72
1.42-1.430.24541180.21772081X-RAY DIFFRACTION75
1.43-1.450.2366920.20092208X-RAY DIFFRACTION82
1.45-1.470.25071200.1922391X-RAY DIFFRACTION87
1.47-1.490.23981350.17842568X-RAY DIFFRACTION94
1.49-1.510.23091250.16522646X-RAY DIFFRACTION96
1.51-1.540.2171480.17072671X-RAY DIFFRACTION99
1.54-1.560.21851220.1592674X-RAY DIFFRACTION98
1.56-1.580.181570.15742734X-RAY DIFFRACTION100
1.58-1.610.20561370.14342739X-RAY DIFFRACTION99
1.61-1.640.22741170.13652783X-RAY DIFFRACTION100
1.64-1.670.17471310.1312717X-RAY DIFFRACTION100
1.67-1.710.17881590.1252717X-RAY DIFFRACTION100
1.71-1.740.18821530.12372745X-RAY DIFFRACTION100
1.74-1.780.17761530.12462691X-RAY DIFFRACTION100
1.78-1.830.16641390.13692758X-RAY DIFFRACTION100
1.83-1.880.16031580.13722724X-RAY DIFFRACTION100
1.88-1.930.19031450.13642757X-RAY DIFFRACTION100
1.93-20.17561670.13592730X-RAY DIFFRACTION100
2-2.070.18151500.13352763X-RAY DIFFRACTION100
2.07-2.150.15551290.12962763X-RAY DIFFRACTION100
2.15-2.250.15571850.12712739X-RAY DIFFRACTION100
2.25-2.370.16861360.13372774X-RAY DIFFRACTION100
2.37-2.520.16061530.1452766X-RAY DIFFRACTION100
2.52-2.710.16541510.14812787X-RAY DIFFRACTION100
2.71-2.980.17981620.16142786X-RAY DIFFRACTION100
2.98-3.410.19771440.16982818X-RAY DIFFRACTION100
3.41-4.30.17821560.15772833X-RAY DIFFRACTION100
4.3-60.410.22991650.20692977X-RAY DIFFRACTION100

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