[English] 日本語
Yorodumi
- PDB-2dsb: Crystal structure of human ADP-ribose pyrophosphatase NUDT5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dsb
TitleCrystal structure of human ADP-ribose pyrophosphatase NUDT5
ComponentsADP-sugar pyrophosphatase
KeywordsHYDROLASE / Nudix domain / ADPR / ADP-ribose pyrophosphatase / NUDT5
Function / homology
Function and homology information


ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process ...ADP-D-ribose pyrophosphorylase / ribonucleoside diphosphate catabolic process / ADP-ribose diphosphatase / nucleobase-containing small molecule metabolic process / 8-oxo-dGDP phosphatase / ADP-ribose diphosphatase activity / D-ribose catabolic process / ADP-sugar diphosphatase activity / nucleoside phosphate metabolic process / ribose phosphate metabolic process / 8-oxo-GDP phosphatase activity / 8-oxo-dGDP phosphatase activity / Phosphate bond hydrolysis by NUDT proteins / ATP generation from poly-ADP-D-ribose / nucleotide metabolic process / snoRNA binding / nucleotidyltransferase activity / chromatin remodeling / magnesium ion binding / protein homodimerization activity / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
NUDIX hydrolase / 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
ADP-sugar pyrophosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsZha, M. / Zhong, C. / Ding, J.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structures of Human NUDT5 Reveal Insights into the Structural Basis of the Substrate Specificity
Authors: Zha, M. / Zhong, C. / Peng, Y. / Hu, H. / Ding, J.
History
DepositionJun 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)101,7074
Polymers101,7074
Non-polymers00
Water3,927218
1
A: ADP-sugar pyrophosphatase
B: ADP-sugar pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)50,8542
Polymers50,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-45 kcal/mol
Surface area19560 Å2
MethodPISA
2
C: ADP-sugar pyrophosphatase
D: ADP-sugar pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)50,8542
Polymers50,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-54 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.717, 70.316, 87.629
Angle α, β, γ (deg.)90.00, 100.41, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
ADP-sugar pyrophosphatase / Nucleoside diphosphate-linked moiety X motif 5 / Nudix motif 5 / YSA1H


Mass: 25426.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUDT5 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9UKK9, ADP-ribose diphosphatase, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% 2-methyl-2,4-pentanediol, 0.16M sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBSRF 3W1A10.9794, 0.9797, 0.9819
SYNCHROTRONBSRF 3W1A21
Detector
TypeIDDetectorDate
MARRESEARCH1CCDJan 2, 2005
MARRESEARCH2CCDMar 26, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97971
30.98191
411
ReflectionResolution: 2.5→50 Å / Num. all: 34058 / Num. obs: 32826 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 58.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.1
Reflection shellResolution: 2.5→2.59 Å / % possible all: 81.2

-
Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→35.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1249698.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1641 5 %RANDOM
Rwork0.214 ---
obs0.214 32813 96.3 %-
all-34058 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.7218 Å2 / ksol: 0.298892 e/Å3
Displacement parametersBiso mean: 69.6 Å2
Baniso -1Baniso -2Baniso -3
1--9.83 Å20 Å27.69 Å2
2---11.04 Å20 Å2
3---20.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.5→35.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6440 0 0 218 6658
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.397 240 5.1 %
Rwork0.361 4446 -
obs--83.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

+
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://pdbjlc1.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