[English] 日本語
Yorodumi
- PDB-7nnj: Crystal Structure of NUDT4 (Diphosphoinositol polyphosphate phosp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

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-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity ...inositol-5-diphosphate-1,3,4,6-tetrakisphosphate diphosphatase activity / bis(5'-adenosyl)-hexaphosphatase activity / diadenosine pentaphosphate catabolic process / diadenosine hexaphosphate catabolic process / adenosine 5'-(hexahydrogen pentaphosphate) catabolic process / endopolyphosphatase activity / inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity / diphosphoinositol polyphosphate metabolic process / diphosphoinositol-polyphosphate diphosphatase activity / inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity / bis(5'-adenosyl)-pentaphosphatase activity / diadenosine hexaphosphate hydrolase (ATP-forming) / Synthesis of pyrophosphates in the cytosol / diphosphoinositol-polyphosphate diphosphatase / snoRNA binding / calcium-mediated signaling / intracellular signal transduction / metal ion binding / nucleus / cytoplasm / cytosol
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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more