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- PDB-1q33: Crystal structure of human ADP-ribose pyrophosphatase NUDT9 -

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Basic information

Entry
Database: PDB / ID: 1q33
TitleCrystal structure of human ADP-ribose pyrophosphatase NUDT9
ComponentsADP-ribose pyrophosphatase
KeywordsHYDROLASE / NUDIX fold
Function / homology
Function and homology information


ADP catabolic process / nucleobase-containing small molecule metabolic process / ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / Phosphate bond hydrolysis by NUDT proteins / cell junction / nuclear membrane / nuclear body / mitochondrial matrix ...ADP catabolic process / nucleobase-containing small molecule metabolic process / ADP-sugar diphosphatase activity / ADP-ribose diphosphatase / ADP-ribose diphosphatase activity / Phosphate bond hydrolysis by NUDT proteins / cell junction / nuclear membrane / nuclear body / mitochondrial matrix / mitochondrion / extracellular exosome
Similarity search - Function
ADP-ribose pyrophosphatase, mitochondrial / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
beta-D-glucopyranose / ADP-ribose pyrophosphatase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.81 Å
AuthorsShen, B.W. / Perraud, A.L. / Scharenberg, A. / Stoddard, B.L.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Crystal Structure and Mutational Analysis of Human NUDT9
Authors: Shen, B.W. / Perraud, A.L. / Scharenberg, A. / Stoddard, B.L.
History
DepositionJul 28, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ADP-ribose pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0718
Polymers33,3141
Non-polymers7577
Water4,234235
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.837, 87.497, 119.814
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein ADP-ribose pyrophosphatase / pyrophosphatase


Mass: 33314.457 Da / Num. of mol.: 1 / Fragment: RESIDUES 59-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Spleen / Gene: NUDT9 / Plasmid: pET24 / Production host: Escherichia coli (E. coli) / Strain (production host): IRL+ / References: UniProt: Q9BW91, ADP-ribose diphosphatase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium sulfate, TrisHCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 21, 2002
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 1.81→36.76 Å / Num. obs: 36910 / % possible obs: 94.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.3 % / Biso Wilson estimate: 23.1 Å2 / Rsym value: 0.052 / Net I/σ(I): 45.8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.98 % / Mean I/σ(I) obs: 5.54 / Num. unique all: 1295 / Rsym value: 0.358 / % possible all: 66.2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.81→36.54 Å / Isotropic thermal model: anisotropic / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 3690 -random
Rwork0.2013 ---
obs0.2037 36910 94 %-
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.593 Å20 Å20 Å2
2---3.172 Å2-0.421 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.81→36.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2362 0 42 235 2639
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.45
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.9
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
1.81-1.870.26595180.25060.0156454868
1.87-1.950.28266400.22460.058607891

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