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- PDB-8wv3: NUDIX hydrolase from Bacillus methanolicus -

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Basic information

Entry
Database: PDB / ID: 8wv3
TitleNUDIX hydrolase from Bacillus methanolicus
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / NUDIX hydrolase
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
DI(HYDROXYETHYL)ETHER / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesBacillus methanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsMa, B.D. / Kong, X.D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911000 China
CitationJournal: To Be Published
Title: NUDIX hydrolase from Bacillus methanolicus
Authors: Kong, X.D. / Ma, B.D.
History
DepositionOct 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 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
C: ADP-ribose pyrophosphatase
D: ADP-ribose pyrophosphatase
E: ADP-ribose pyrophosphatase
F: ADP-ribose pyrophosphatase
G: ADP-ribose pyrophosphatase
H: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,23512
Polymers170,4598
Non-polymers7774
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.828, 96.884, 103.987
Angle α, β, γ (deg.)90.00, 98.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADP-ribose pyrophosphatase


Mass: 21307.314 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus methanolicus (bacteria) / Gene: act / Production host: Escherichia coli (E. coli) / References: UniProt: I3EA59
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES monohydrate pH 5.2, 18% v/v Polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.98→65.79 Å / Num. obs: 102810 / % possible obs: 97.5 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.041 / Rrim(I) all: 0.098 / Χ2: 0.86 / Net I/σ(I): 11.3 / Num. measured all: 594778
Reflection shellResolution: 1.98→2.08 Å / % possible obs: 90.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.833 / Num. measured all: 81436 / Num. unique obs: 13895 / CC1/2: 0.698 / Rpim(I) all: 0.369 / Rrim(I) all: 0.913 / Χ2: 0.61 / Net I/σ(I) obs: 2.4

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→34.13 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.244 5184 5.06 %
Rwork0.1985 --
obs0.2008 102409 97.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11004 0 45 383 11432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911192
X-RAY DIFFRACTIONf_angle_d0.98315069
X-RAY DIFFRACTIONf_dihedral_angle_d7.4261484
X-RAY DIFFRACTIONf_chiral_restr0.0641747
X-RAY DIFFRACTIONf_plane_restr0.0091923
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-20.33951800.27793308X-RAY DIFFRACTION99
2-2.020.31971650.26823296X-RAY DIFFRACTION100
2.02-2.050.28081560.25453283X-RAY DIFFRACTION100
2.05-2.070.34121140.25852118X-RAY DIFFRACTION86
2.07-2.10.27391780.24192995X-RAY DIFFRACTION97
2.1-2.130.31171830.23533337X-RAY DIFFRACTION100
2.13-2.160.29371860.22293308X-RAY DIFFRACTION100
2.16-2.190.26451720.22743320X-RAY DIFFRACTION100
2.19-2.230.26751940.22923288X-RAY DIFFRACTION100
2.23-2.260.30381150.23822236X-RAY DIFFRACTION67
2.26-2.30.30021680.23213333X-RAY DIFFRACTION100
2.3-2.340.27881820.2243280X-RAY DIFFRACTION100
2.34-2.390.25892070.22413287X-RAY DIFFRACTION100
2.39-2.440.26741660.22943317X-RAY DIFFRACTION100
2.44-2.490.31142030.22023333X-RAY DIFFRACTION100
2.49-2.550.2761720.22123321X-RAY DIFFRACTION100
2.55-2.610.27541580.21773339X-RAY DIFFRACTION100
2.61-2.680.28721680.22843339X-RAY DIFFRACTION100
2.68-2.760.27581880.22823323X-RAY DIFFRACTION100
2.76-2.850.31271800.23243344X-RAY DIFFRACTION100
2.85-2.950.24131730.22913341X-RAY DIFFRACTION100
2.95-3.070.28841900.22733314X-RAY DIFFRACTION100
3.07-3.210.28621640.2273341X-RAY DIFFRACTION100
3.21-3.380.24411610.21083357X-RAY DIFFRACTION100
3.38-3.590.26391690.19843355X-RAY DIFFRACTION100
3.59-3.870.22162080.17713334X-RAY DIFFRACTION100
3.87-4.260.20261840.16393310X-RAY DIFFRACTION100
4.26-4.870.19471840.15343344X-RAY DIFFRACTION100
4.87-6.130.18851460.17283409X-RAY DIFFRACTION100
6.13-34.130.20661700.17373415X-RAY DIFFRACTION99

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