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

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Basic information

Entry
Database: PDB / ID: 9duf
TitleCrystal structure of ADP-ribose diphosphatase from Klebsiella pneumoniae (FMN 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
FLAVIN MONONUCLEOTIDE / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 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 (FMN bound)
Authors: Enayati, P. / 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)50,5209
Polymers49,4862
Non-polymers1,0347
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9080 Å2
ΔGint-84 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.374, 79.575, 91.903
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-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 492 / 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: 41.97 %
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. plaate Liu-S-107 AB/12 ApoSoak. 5 hour soak in 7mM FMN. Puck: PSL-2111, Cryo: 30% (v/v) PEG ...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. plaate Liu-S-107 AB/12 ApoSoak. 5 hour soak in 7mM FMN. Puck: PSL-2111, 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: Aug 3, 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: 1.32→48.67 Å / Num. obs: 99375 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.016 / Rrim(I) all: 0.057 / Χ2: 1.01 / Net I/σ(I): 22.4 / Num. measured all: 1256187
Reflection shellResolution: 1.32→1.34 Å / % possible obs: 99.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 1.15 / Num. measured all: 34479 / Num. unique obs: 4818 / CC1/2: 0.648 / Rpim(I) all: 0.448 / Rrim(I) all: 1.24 / Χ2: 1 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX(dev_5449: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→48.67 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1658 5018 5.05 %
Rwork0.1415 --
obs0.1428 99281 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.32→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3250 0 67 492 3809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073522
X-RAY DIFFRACTIONf_angle_d0.9594809
X-RAY DIFFRACTIONf_dihedral_angle_d13.8131305
X-RAY DIFFRACTIONf_chiral_restr0.08525
X-RAY DIFFRACTIONf_plane_restr0.009627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.32-1.330.30221420.2593088X-RAY DIFFRACTION99
1.34-1.350.24081510.23683097X-RAY DIFFRACTION100
1.35-1.370.27371640.21763132X-RAY DIFFRACTION100
1.37-1.380.23371650.19453086X-RAY DIFFRACTION100
1.38-1.40.25381740.17633120X-RAY DIFFRACTION100
1.4-1.420.22351590.16783096X-RAY DIFFRACTION100
1.42-1.440.21650.15833126X-RAY DIFFRACTION100
1.44-1.460.18091710.15723118X-RAY DIFFRACTION100
1.46-1.490.18641500.15693104X-RAY DIFFRACTION100
1.49-1.510.18861670.15063116X-RAY DIFFRACTION100
1.51-1.540.17281720.14313105X-RAY DIFFRACTION100
1.54-1.570.18581770.13973123X-RAY DIFFRACTION100
1.57-1.60.16121710.13123107X-RAY DIFFRACTION100
1.6-1.630.17951630.12073111X-RAY DIFFRACTION100
1.63-1.660.16461540.11863156X-RAY DIFFRACTION100
1.66-1.70.14431470.10963146X-RAY DIFFRACTION100
1.7-1.740.15071720.12063107X-RAY DIFFRACTION100
1.74-1.790.16141640.1283162X-RAY DIFFRACTION100
1.79-1.840.17781680.13773107X-RAY DIFFRACTION100
1.84-1.90.17391850.14353134X-RAY DIFFRACTION100
1.9-1.970.16821800.13853132X-RAY DIFFRACTION100
1.97-2.050.16211530.12783154X-RAY DIFFRACTION100
2.05-2.140.15781680.12563150X-RAY DIFFRACTION100
2.14-2.260.13951890.12543146X-RAY DIFFRACTION100
2.26-2.40.1471600.13133175X-RAY DIFFRACTION100
2.4-2.580.15671890.13253151X-RAY DIFFRACTION100
2.58-2.840.16611610.14153194X-RAY DIFFRACTION100
2.84-3.250.16051760.1453188X-RAY DIFFRACTION100
3.26-4.10.15131810.14043255X-RAY DIFFRACTION100
4.1-48.670.1711800.15223377X-RAY DIFFRACTION100

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