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- PDB-9jax: Crystal structure of NUDIX hydrolase from Bacillus methanolicus -

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Basic information

Entry
Database: PDB / ID: 9jax
TitleCrystal structure of NUDIX hydrolase from Bacillus methanolicus
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / NUDIX hydrolase
Function / homology
Function and homology information


ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 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
polyethylene glycol / DI(HYDROXYETHYL)ETHER / ADP-ribose pyrophosphatase
Similarity search - Component
Biological speciesBacillus methanolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKong, X.D. / Ma, B.D.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0911000 China
CitationJournal: To Be Published
Title: Crystal structure of NUDIX hydrolase from Bacillus methanolicus
Authors: Kong, X.D. / Ma, B.D.
History
DepositionAug 25, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: ADP-ribose pyrophosphatase
A: ADP-ribose pyrophosphatase
B: ADP-ribose pyrophosphatase
C: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,6169
Polymers87,4404
Non-polymers1,1765
Water3,405189
1
E: ADP-ribose pyrophosphatase
A: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1275
Polymers43,7202
Non-polymers4073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-24 kcal/mol
Surface area17070 Å2
MethodPISA
2
B: ADP-ribose pyrophosphatase
C: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4894
Polymers43,7202
Non-polymers7692
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-34 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.710, 98.310, 73.500
Angle α, β, γ (deg.)90.00, 110.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ADP-ribose pyrophosphatase


Mass: 21859.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus methanolicus (bacteria) / Gene: act, BMMGA3_11130 / Production host: Escherichia coli (E. coli) / References: UniProt: I3EA59, ADP-ribose diphosphatase
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H62O15
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MMT buffer pH 5.0, PEG 1500

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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: Nov 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.4→98.31 Å / Num. obs: 31100 / % possible obs: 99.7 % / Redundancy: 6.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.034 / Rrim(I) all: 0.087 / Χ2: 1.06 / Net I/σ(I): 15.7 / Num. measured all: 204575
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.663 / Num. measured all: 21232 / Num. unique obs: 3256 / CC1/2: 0.88 / Rpim(I) all: 0.279 / Rrim(I) all: 0.72 / Χ2: 0.97 / Net I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→68.89 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2392 1540 4.96 %
Rwork0.1865 --
obs0.1891 31046 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→68.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5754 0 0 189 5943
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085825
X-RAY DIFFRACTIONf_angle_d0.9867822
X-RAY DIFFRACTIONf_dihedral_angle_d22.2172299
X-RAY DIFFRACTIONf_chiral_restr0.056899
X-RAY DIFFRACTIONf_plane_restr0.007992
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.33561650.2572624X-RAY DIFFRACTION100
2.48-2.570.3181430.23022673X-RAY DIFFRACTION100
2.57-2.670.3041360.22382697X-RAY DIFFRACTION100
2.67-2.790.28981290.22712650X-RAY DIFFRACTION100
2.79-2.940.33191300.24192725X-RAY DIFFRACTION100
2.94-3.120.33831310.22332675X-RAY DIFFRACTION100
3.12-3.360.26291550.20992688X-RAY DIFFRACTION100
3.36-3.70.27471260.18962702X-RAY DIFFRACTION100
3.7-4.240.19261530.16792692X-RAY DIFFRACTION100
4.24-5.340.17481590.14892659X-RAY DIFFRACTION100
5.34-68.890.2161130.16682721X-RAY DIFFRACTION98

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