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- PDB-5ltu: Crystal Structure of NUDT4A- Diphosphoinositol polyphosphate phos... -

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Basic information

Entry
Database: PDB / ID: 5ltu
TitleCrystal Structure of NUDT4A- Diphosphoinositol polyphosphate phosphohydrolase 2
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 2
KeywordsHYDROLASE / Diphosphoinositol polyphosphate phosphohydrolase 2
Function / homology
Function and homology information


: / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase ...: / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / endopolyphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diphosphoinositol polyphosphate metabolic process / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / diphosphoinositol-polyphosphate diphosphatase / diphosphoinositol-polyphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / bis(5'-adenosyl)-pentaphosphatase activity / snoRNA binding / calcium-mediated signaling / intracellular signal transduction / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
: / NUDIX hydrolase, conserved site / Nudix box signature. / 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
Diphosphoinositol polyphosphate phosphohydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.23 Å
AuthorsSrikannathasan, V. / Nunez, C.A. / Tallant, C. / Siejka, P. / Mathea, S. / Newman, J. / Strain-Damerell, C. / Elkins, J.M. / Burgess-Brown, N. / Arrowsmith, C.H. ...Srikannathasan, V. / Nunez, C.A. / Tallant, C. / Siejka, P. / Mathea, S. / Newman, J. / Strain-Damerell, C. / Elkins, J.M. / Burgess-Brown, N. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / von Delft, F. / Huber, K.
CitationJournal: To Be Published
Title: Crystal Structure of Human NUDT4A- Diphosphoinositol polyphosphate phosphohydrolase 2
Authors: Srikannathasan, V. / Huber, K.
History
DepositionSep 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Diphosphoinositol polyphosphate phosphohydrolase 2
B: Diphosphoinositol polyphosphate phosphohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,16510
Polymers40,6682
Non-polymers4978
Water1,58588
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint16 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.710, 41.030, 74.320
Angle α, β, γ (deg.)90.000, 122.550, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and segid AA
21chain B and segid BA

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and segid AAA0
211chain B and segid BAB0

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Components

#1: Protein Diphosphoinositol polyphosphate phosphohydrolase 2 / DIPP-2 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 2 / Nucleoside diphosphate-linked ...DIPP-2 / Diadenosine 5' / 5'''-P1 / P6-hexaphosphate hydrolase 2 / Nucleoside diphosphate-linked moiety X motif 4 / Nudix motif 4


Mass: 20334.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT4, DIPP2, KIAA0487, HDCMB47P / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NZJ9, diphosphoinositol-polyphosphate diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.64 % / Description: Needle
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2M Ammonium Sulphate, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Nov 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.23→62 Å / Num. obs: 17028 / % possible obs: 98.7 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 12.8
Reflection shellResolution: 2.23→2.29 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.051 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.998 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
MOLREPphasing
PHENIX1.9_1682refinement
PDB_EXTRACT3.2data extraction
Aimlessdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2duk

2duk


Resolution: 2.23→61.997 Å / SU ML: 0.28 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.44
RfactorNum. reflection% reflection
Rfree0.2449 922 5.42 %
Rwork0.2155 --
obs0.2173 17026 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 190.72 Å2 / Biso mean: 51.9099 Å2 / Biso min: 19.69 Å2
Refinement stepCycle: final / Resolution: 2.23→61.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 32 88 2078
Biso mean--82.97 56.85 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032017
X-RAY DIFFRACTIONf_angle_d0.9422707
X-RAY DIFFRACTIONf_chiral_restr0.039297
X-RAY DIFFRACTIONf_plane_restr0.003346
X-RAY DIFFRACTIONf_dihedral_angle_d14.747722
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1088X-RAY DIFFRACTION8.44TORSIONAL
12B1088X-RAY DIFFRACTION8.44TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2301-2.34770.31221300.27522280241099
2.3477-2.49480.33641190.268622952414100
2.4948-2.68740.31031200.25432281240199
2.6874-2.95780.31471240.24262313243799
2.9578-3.38580.23651330.21682304243799
3.3858-4.26560.21261420.18352271241399
4.2656-62.02120.2221540.20442360251499
Refinement TLS params.Method: refined / Origin x: -10.4488 Å / Origin y: 3.5746 Å / Origin z: 15.9172 Å
111213212223313233
T0.2748 Å20.0119 Å20.065 Å2-0.1799 Å2-0.021 Å2--0.2819 Å2
L3.8526 °2-0.3464 °22.9274 °2-0.2577 °2-0.4025 °2--2.3123 °2
S-0.083 Å °-0.0223 Å °0.0853 Å °-0.0145 Å °0.0701 Å °-0.0827 Å °-0.066 Å °0.0213 Å °0.0182 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA9 - 146
2X-RAY DIFFRACTION1allB8 - 147
3X-RAY DIFFRACTION1allS1 - 89
4X-RAY DIFFRACTION1allC1 - 4
5X-RAY DIFFRACTION1allC5 - 7
6X-RAY DIFFRACTION1allC8

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