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- PDB-7nnj: Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosp... -

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Entry
Database: PDB / ID: 7nnj
TitleCrystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-Bn-1-PCP-InsP4 (AMR2105)
ComponentsDiphosphoinositol polyphosphate phosphohydrolase 2
KeywordsHYDROLASE / NUDIX / 1-InsP7 analogue
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 / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol ...inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / Synthesis of pyrophosphates in the cytosol / bis(5'-adenosyl)-pentaphosphatase activity / diphosphoinositol-polyphosphate diphosphatase / snoRNA binding / calcium-mediated signaling / intracellular signal transduction / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / 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
FORMIC ACID / Chem-UJN / Diphosphoinositol polyphosphate phosphohydrolase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.755 Å
AuthorsDubianok, Y. / Arruda Bezerra, G. / Raux, B. / Diaz Saez, L. / Riley, A.M. / Potter, B.V.L. / Huber, K.V.M. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Innovative Medicines Initiative875510 United Kingdom
CitationJournal: To Be Published
Title: Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosphohydrolase 2) in complex with 4-O-Bn-1-PCP-InsP4 (AMR2105)
Authors: Riley, A.M. / Raux, B. / Diaz Saez, L. / Dubianok, Y. / Arruda Bezerra, G. / von Delft, F. / Huber, K.V.M. / Potter, B.V.L.
History
DepositionFeb 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)33,54111
Polymers32,3772
Non-polymers1,1659
Water1,892105
1
A: Diphosphoinositol polyphosphate phosphohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4516
Polymers16,1881
Non-polymers2625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diphosphoinositol polyphosphate phosphohydrolase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0915
Polymers16,1881
Non-polymers9024
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.181, 40.772, 197.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 16188.368 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT4, DIPP2, KIAA0487, HDCMB47P / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NZJ9, diphosphoinositol-polyphosphate diphosphatase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-UJN / [oxidanyl-[(2S,3R,5S,6S)-4-phenylmethoxy-2,3,5,6-tetraphosphonooxy-cyclohexyl]oxy-phosphoryl]methylphosphonic acid / [oxidanyl-[(2~{S},3~{R},5~{S},6~{S})-4-phenylmethoxy-2,3,5,6-tetraphosphonooxy-cyclohexyl]oxy-phosphoryl]methylphosphonic acid


Mass: 748.185 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H26O23P6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2.75 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.755→98.844 Å / Num. obs: 24365 / % possible obs: 91.5 % / Redundancy: 25.3 % / Biso Wilson estimate: 31.52 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.021 / Rrim(I) all: 0.105 / Net I/σ(I): 21.7 / Num. measured all: 617285
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.755-1.92625.12.73063412190.610.5472.7561.556.1
5.541-98.84421.60.0426322121810.0090.04170.7100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.55 Å98.84 Å
Translation6.55 Å98.84 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.27data extraction
Aimlessdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TLU

5tlu


Resolution: 1.755→39.932 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2447 1266 5.2 %
Rwork0.1949 23093 -
obs0.1976 24359 72.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.57 Å2 / Biso mean: 47.3846 Å2 / Biso min: 19.62 Å2
Refinement stepCycle: final / Resolution: 1.755→39.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2082 0 70 105 2257
Biso mean--63.88 49.09 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082190
X-RAY DIFFRACTIONf_angle_d1.072954
X-RAY DIFFRACTIONf_chiral_restr0.043315
X-RAY DIFFRACTIONf_plane_restr0.005372
X-RAY DIFFRACTIONf_dihedral_angle_d14.794809
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.755-1.82530.383250.31421424
1.8253-1.90840.2892320.290176722
1.9084-2.0090.3176720.2657170249
2.009-2.13490.32611390.2573271877
2.1349-2.29970.30531680.237338897
2.2997-2.53110.33291990.22873523100
2.5311-2.89720.24512220.22853526100
2.8972-3.64980.26371940.18633579100
3.6498-39.90.19752350.16073748100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.48635.57634.19516.28095.4646.83570.29590.026-0.11950.3653-0.1792-0.08450.3473-0.0174-0.14090.31020.0564-0.06140.1316-0.01020.2853-1.219-17.71844.8237
29.0551-0.95510.37457.1213-0.83399.22620.26630.0258-0.2332-0.3574-0.14570.7229-0.0639-1.193-0.00830.2392-0.0253-0.1130.33960.02650.2712-15.9286-24.632234.8249
34.5310.0196-0.05843.7393-1.71145.47970.1776-0.2484-0.14240.2877-0.0245-0.14250.0065-0.2446-0.18530.2515-0.0059-0.06520.1170.00310.2135-6.2468-27.103346.2551
46.0081-2.15731.645810.11075.42068.7929-0.45750.17130.6265-0.48270.27530.4821-1.5960.2580.34170.4772-0.0334-0.00920.19020.05190.2896-0.2435-14.518837.8487
53.45771.6941.30894.8386-0.82775.04830.4629-0.188-0.03650.444-0.11810.75640.4944-0.6752-0.33590.3466-0.0272-0.03670.23710.00670.3543-9.8364-27.764840.9362
65.5296-0.05321.29717.30741.39388.74120.06730.12870.2098-0.6108-0.01280.7956-0.4126-1.0228-0.02610.30860.0481-0.11230.37840.05330.3664-16.4998-22.269329.2175
78.3966-3.117-2.40656.94752.80027.26540.13130.65380.0723-0.4963-0.0180.1323-0.68140.1944-0.14180.36720.0094-0.07280.27420.05520.2096-5.7771-19.311929.5021
83.98640.0729-4.67481.0108-0.37134.4067-0.11490.2363-0.20010.05780.0868-0.0863-0.1538-0.20320.08480.23660.0284-0.02320.65080.05850.338113.7966-8.71753.703
98.69160.25095.0919.1804-8.20462.0529-0.3073-0.08920.57240.1934-0.32460.7890.1116-0.61590.40570.64690.36920.24950.85860.05190.5947-2.9848-5.521723.304
102.9392-1.58163.61443.6596-1.81975.22790.23880.1573-0.4270.13240.1705-0.53570.27710.4295-0.39920.41050.1081-0.05190.61040.00730.430312.5685-16.875120.5787
114.59010.48291.71285.19593.78317.6975-1.4225-0.0761-0.6844-1.1811.2755-0.24450.11370.16320.02510.08870.07510.03840.91970.1590.338.61-12.2929-0.1824
120.6551.7991-0.39733.2572-0.56073.4579-0.2086-0.0012-0.12310.07280.38860.11650.1258-0.2757-0.18370.22530.07320.00830.53960.09890.3932.6197-13.72089.5367
130.7395-0.74161.5476.6215-2.58524.1825-0.9978-1.09280.685-0.50281.5828-1.3311-1.72971.98740.02980.2416-0.0208-0.08170.6885-0.07090.386116.4514-2.8689.3258
140.372-0.0972-1.51835.1892-2.21624.5929-0.00570.8220.09180.260.48610.3789-0.1708-0.2349-0.42130.26270.1269-0.05710.68510.08710.29684.3165-8.760411.3679
153.0256-0.86551.23140.2041-0.43860.61620.71651.4881-1.5769-0.55680.002-0.1990.42280.6061-0.67990.42270.02710.00590.7088-0.0840.82014.7167-25.00416.4163
168.28565.00461.34888.15091.45353.76430.0937-0.8085-0.18081.2382-0.12310.1793-0.2802-0.1251-0.03260.55810.15250.01760.59220.11840.317.8029-10.565626.1234
173.165-5.9484-0.092.7988-1.36584.3469-0.1358-0.49550.44510.74740.1395-0.7596-0.2680.2215-0.05750.39440.0355-0.09470.44820.04790.478513.7988-3.835419.9684
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 26 )A9 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 49 )A27 - 49
3X-RAY DIFFRACTION3chain 'A' and (resid 50 through 79 )A50 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 90 )A80 - 90
5X-RAY DIFFRACTION5chain 'A' and (resid 91 through 115 )A91 - 115
6X-RAY DIFFRACTION6chain 'A' and (resid 116 through 132 )A116 - 132
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 146 )A133 - 146
8X-RAY DIFFRACTION8chain 'B' and (resid 8 through 26 )B8 - 26
9X-RAY DIFFRACTION9chain 'B' and (resid 27 through 32 )B27 - 32
10X-RAY DIFFRACTION10chain 'B' and (resid 33 through 49 )B33 - 49
11X-RAY DIFFRACTION11chain 'B' and (resid 50 through 58 )B50 - 58
12X-RAY DIFFRACTION12chain 'B' and (resid 59 through 79 )B59 - 79
13X-RAY DIFFRACTION13chain 'B' and (resid 80 through 90 )B80 - 90
14X-RAY DIFFRACTION14chain 'B' and (resid 91 through 103 )B91 - 103
15X-RAY DIFFRACTION15chain 'B' and (resid 104 through 116 )B104 - 116
16X-RAY DIFFRACTION16chain 'B' and (resid 117 through 129 )B117 - 129
17X-RAY DIFFRACTION17chain 'B' and (resid 130 through 145 )B130 - 145

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