[English] 日本語
Yorodumi
- PDB-9fl6: Human NUDT1 with medetomidine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fl6
TitleHuman NUDT1 with medetomidine
ComponentsIsoform p26 of Oxidized purine nucleoside triphosphate hydrolase
KeywordsHYDROLASE / Nudix hydrolase
Function / homology
Function and homology information


2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins ...2-hydroxy-ATP hydrolase activity / 2-hydroxy-dATP hydrolase activity / N6-methyl-(d)ATP hydrolase activity / O6-methyl-dGTP hydrolase activity / 2-hydroxy-dATP diphosphatase / dATP diphosphatase activity / ATP diphosphatase activity / 8-oxo-7,8-dihydrodeoxyguanosine triphosphate pyrophosphatase activity / 8-oxo-7,8-dihydroguanosine triphosphate pyrophosphatase activity / Phosphate bond hydrolysis by NUDT proteins / DNA protection / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / purine nucleoside catabolic process / snoRNA binding / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / response to cadmium ion / acrosomal vesicle / male gonad development / nuclear membrane / response to oxidative stress / mitochondrial matrix / DNA repair / mitochondrion / extracellular space / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Oxidized purine nucleoside triphosphate / NUDIX hydrolase / 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
: / ACETATE ION / Oxidized purine nucleoside triphosphate hydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSalah, E. / Huber, K.V.M. / Elkins, J.M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: NUDT1 with medetomidine
Authors: Salah, E. / Huber, K.V.M. / Elkins, J.M.
History
DepositionJun 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Isoform p26 of Oxidized purine nucleoside triphosphate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3593
Polymers18,1001
Non-polymers2592
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area8220 Å2
Unit cell
Length a, b, c (Å)36.739, 60.850, 67.530
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

-
Components

#1: Protein Isoform p26 of Oxidized purine nucleoside triphosphate hydrolase / 2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / ...2-hydroxy-dATP diphosphatase / 7 / 8-dihydro-8-oxoguanine triphosphatase / 8-oxo-dGTPase / Methylated purine nucleoside triphosphate hydrolase / Nucleoside diphosphate-linked moiety X motif 1 / Nudix motif 1


Mass: 18099.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: NUDT1, Nudix hydrolase 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT1, MTH1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P36639, 2-hydroxy-dATP diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Chemical ChemComp-A1IFR / 5-[(1~{R})-1-(2,3-dimethylphenyl)ethyl]-1~{H}-imidazole / (R)-4-(1-(2,3-dimethylphenyl)ethyl)-1H-imidazole / Medetomidine


Mass: 200.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H16N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 30% PEG8000, 0.2 M lithium sulfate and 0.1 M acetate pH 4.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 1.3→67.53 Å / Num. obs: 38033 / % possible obs: 99.9 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 13.4
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.693 / Num. unique obs: 1936 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→45.205 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.947 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.053 / ESU R Free: 0.055
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2065 1935 5.097 %
Rwork0.1592 36025 -
all0.161 --
obs-37960 99.868 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 16.151 Å2
Baniso -1Baniso -2Baniso -3
1-0.413 Å20 Å2-0 Å2
2---0.492 Å20 Å2
3---0.078 Å2
Refinement stepCycle: LAST / Resolution: 1.3→45.205 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1246 0 19 132 1397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0131381
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151272
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.6451885
X-RAY DIFFRACTIONr_angle_other_deg1.3111.5972938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3155174
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.71422.30878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.71815232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.251159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_nbd_refined0.2020.2161
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.21047
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2574
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.264
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2860.29
X-RAY DIFFRACTIONr_nbd_other0.1440.227
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1160.213
X-RAY DIFFRACTIONr_mcbond_it1.2541.433653
X-RAY DIFFRACTIONr_mcbond_other1.2411.432651
X-RAY DIFFRACTIONr_mcangle_it1.7512.162824
X-RAY DIFFRACTIONr_mcangle_other1.7552.162825
X-RAY DIFFRACTIONr_scbond_it1.6831.72727
X-RAY DIFFRACTIONr_scbond_other1.6821.72728
X-RAY DIFFRACTIONr_scangle_it2.1842.4791055
X-RAY DIFFRACTIONr_scangle_other2.1842.4791056
X-RAY DIFFRACTIONr_lrange_it2.96817.0021372
X-RAY DIFFRACTIONr_lrange_other2.96717.0071373
X-RAY DIFFRACTIONr_rigid_bond_restr1.11832652
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.3-1.3340.2661500.2625800.26127540.8560.85299.12850.249
1.334-1.370.2741290.23525740.23727060.8710.8899.88910.221
1.37-1.410.2391250.2224900.22126170.8880.89799.92360.203
1.41-1.4530.2241310.1824210.18325540.9240.93299.92170.163
1.453-1.5010.1831270.1523460.15224730.9510.9531000.131
1.501-1.5540.2051200.13722840.1424040.9380.9581000.119
1.554-1.6120.1781240.13621860.13923190.9480.96199.61190.118
1.612-1.6780.2081160.13521260.13822420.9450.9591000.118
1.678-1.7520.1741070.12420390.12721480.9640.97199.90690.109
1.752-1.8380.1911030.12619450.1320490.950.96999.95120.115
1.838-1.9370.1641170.12618440.12819610.9650.9751000.115
1.937-2.0540.201880.13917600.14218540.9570.9799.67640.131
2.054-2.1960.158820.14316690.14317510.9730.9711000.137
2.196-2.3710.19980.14615360.14916340.9590.971000.145
2.371-2.5970.18740.15514530.15615270.9640.9641000.155
2.597-2.9020.201830.17912950.18113780.9510.9591000.185
2.902-3.3490.169550.16711840.16712390.9660.9671000.181
3.349-4.0960.219450.14910040.15110500.950.97499.90480.17
4.096-5.7690.266330.1578030.1618360.9550.9751000.189
5.769-45.2050.403280.2494850.2565130.9340.9411000.288

+
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