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- PDB-9b1z: Crystal structure of ADP-ribose diphosphatase from Klebsiella pne... -

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Basic information

Entry
Database: PDB / ID: 9b1z
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (Apo)
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
ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 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 (Apo)
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)49,5324
Polymers49,4862
Non-polymers462
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7420 Å2
ΔGint-58 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.696, 74.289, 58.021
Angle α, β, γ (deg.)90.00, 115.80, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.99 Å3/Da / Density % sol: 38.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 33% Peg 3350, 0.1M Tris, pH 8.5, 0.2 M sodium acetate, KlpnC.20447.a.B1.PB00133 at 26 mg/mL. plate Liu-S-102, C1. Puck: PSL-1001, Cryo: direct.

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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: 1.25→45.58 Å / Num. obs: 99570 / % possible obs: 93.3 % / Redundancy: 6.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.038 / Rrim(I) all: 0.096 / Χ2: 0.91 / Net I/σ(I): 15 / Num. measured all: 609044
Reflection shellResolution: 1.25→1.28 Å / % possible obs: 55 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.441 / Num. measured all: 11802 / Num. unique obs: 4291 / CC1/2: 0.717 / Rpim(I) all: 0.302 / Rrim(I) all: 0.539 / Χ2: 0.95 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
PHENIX(dev_5243: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→45.58 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1455 5016 5.04 %
Rwork0.1181 --
obs0.1195 99539 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.25→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 2 573 3791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073423
X-RAY DIFFRACTIONf_angle_d0.9594675
X-RAY DIFFRACTIONf_dihedral_angle_d13.7011294
X-RAY DIFFRACTIONf_chiral_restr0.084523
X-RAY DIFFRACTIONf_plane_restr0.011613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.260.3736780.32691673X-RAY DIFFRACTION49
1.26-1.280.2598910.19161982X-RAY DIFFRACTION59
1.28-1.290.18931220.13832171X-RAY DIFFRACTION65
1.29-1.310.18271320.12992457X-RAY DIFFRACTION73
1.31-1.330.15111530.12412705X-RAY DIFFRACTION80
1.33-1.350.1821480.12522938X-RAY DIFFRACTION86
1.35-1.370.15871670.11953082X-RAY DIFFRACTION93
1.37-1.390.15461740.11623281X-RAY DIFFRACTION97
1.39-1.410.15251630.11693319X-RAY DIFFRACTION98
1.41-1.430.1441920.11373329X-RAY DIFFRACTION100
1.43-1.460.1731830.10753396X-RAY DIFFRACTION100
1.46-1.480.12942060.10023299X-RAY DIFFRACTION100
1.48-1.510.12411970.09583350X-RAY DIFFRACTION100
1.51-1.540.14141960.09353384X-RAY DIFFRACTION100
1.54-1.570.12831920.09393358X-RAY DIFFRACTION100
1.57-1.610.13121580.09733394X-RAY DIFFRACTION100
1.61-1.650.12551780.09743383X-RAY DIFFRACTION100
1.65-1.70.13231470.09723393X-RAY DIFFRACTION100
1.7-1.750.14541980.10023388X-RAY DIFFRACTION100
1.75-1.80.13011720.10463369X-RAY DIFFRACTION100
1.8-1.870.13741740.10833372X-RAY DIFFRACTION100
1.87-1.940.13851900.10863387X-RAY DIFFRACTION100
1.94-2.030.13541800.10823347X-RAY DIFFRACTION100
2.03-2.140.12571730.10393423X-RAY DIFFRACTION100
2.14-2.270.14121600.10943369X-RAY DIFFRACTION100
2.27-2.450.12121670.11593409X-RAY DIFFRACTION100
2.45-2.690.12762200.11823394X-RAY DIFFRACTION100
2.69-3.080.17561510.13223394X-RAY DIFFRACTION100
3.08-3.880.12981440.12693374X-RAY DIFFRACTION97
3.88-45.580.17252100.14363403X-RAY DIFFRACTION99

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