[English] 日本語
Yorodumi
- PDB-3p48: Structure of the yeast dUTPase DUT1 in complex with dUMPNPP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3p48
TitleStructure of the yeast dUTPase DUT1 in complex with dUMPNPP
ComponentsDeoxyuridine 5'-triphosphate nucleotidohydrolase
KeywordsHYDROLASE / TRIMER / BETA BARREL / DUMPPNP PYROPHOSPHATASE / PHOSPHOPROTEIN / Structural Genomics / Ontario Centre for Structural Proteomics / OCSP
Function / homology
Function and homology information


pyrimidine deoxyribonucleoside triphosphate catabolic process / dITP catabolic process / dITP diphosphatase activity / Interconversion of nucleotide di- and triphosphates / dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding / nucleus / cytoplasm
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / Deoxyuridine triphosphatase (dUTPase) / Deoxyuridine 5'-Triphosphate Nucleotidohydrolase; Chain A / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsPetit, P. / Singer, A.U. / Evdokimova, E. / Kudritska, M. / Edwards, A.M. / Yakunin, A.F. / Savchenko, A. / Ontario Centre for Structural Proteomics (OCSP)
CitationJournal: Biochem.J. / Year: 2011
Title: Structure and activity of the Saccharomyces cerevisiae dUTP pyrophosphatase DUT1, an essential housekeeping enzyme.
Authors: Tchigvintsev, A. / Singer, A.U. / Flick, R. / Petit, P. / Brown, G. / Evdokimova, E. / Savchenko, A. / Yakunin, A.F.
History
DepositionOct 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2012Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyuridine 5'-triphosphate nucleotidohydrolase
B: Deoxyuridine 5'-triphosphate nucleotidohydrolase
C: Deoxyuridine 5'-triphosphate nucleotidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4449
Polymers45,9703
Non-polymers1,4746
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10990 Å2
ΔGint-90 kcal/mol
Surface area14380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.784, 58.868, 112.381
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Deoxyuridine 5'-triphosphate nucleotidohydrolase / dUTPase / dUTP pyrophosphatase


Mass: 15323.264 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: DUT1, YBR252W, YBR1705 / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33317, dUTP diphosphatase
#2: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 33.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% Jeffamine ED-2001, 0.1M HEPES pH7, 3mM MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 24, 2010
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.67→29.43 Å / Num. all: 42235 / Num. obs: 40597 / % possible obs: 96.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.043 / Rsym value: 0.039 / Net I/σ(I): 28.4
Reflection shellResolution: 1.67→1.76 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 8.2 / Rsym value: 0.219 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F4F

3f4f


Resolution: 1.67→28.47 Å / SU ML: 0.16 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.193 2017 5.02 %
Rwork0.154 --
obs0.156 40218 99 %
all-42235 -
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.12 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.552 Å2-0 Å20 Å2
2---1.9019 Å2-0 Å2
3---2.4539 Å2
Refinement stepCycle: LAST / Resolution: 1.67→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2834 0 87 405 3326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172969
X-RAY DIFFRACTIONf_angle_d1.6564052
X-RAY DIFFRACTIONf_dihedral_angle_d17.2991151
X-RAY DIFFRACTIONf_chiral_restr0.115489
X-RAY DIFFRACTIONf_plane_restr0.008501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.72970.24051970.17143643X-RAY DIFFRACTION96
1.7297-1.79890.24122170.16783675X-RAY DIFFRACTION97
1.7989-1.88080.22131910.16093735X-RAY DIFFRACTION98
1.8808-1.97990.20111960.14653804X-RAY DIFFRACTION99
1.9799-2.10390.19741680.14443851X-RAY DIFFRACTION100
2.1039-2.26630.2011900.14713842X-RAY DIFFRACTION100
2.2663-2.49430.17822110.13993809X-RAY DIFFRACTION100
2.4943-2.85490.20312100.15583878X-RAY DIFFRACTION100
2.8549-3.59580.1862100.15883902X-RAY DIFFRACTION100
3.5958-28.47770.17522270.15684062X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -16.1363 Å / Origin y: 23.9835 Å / Origin z: -18.7383 Å
111213212223313233
T0.0449 Å20.003 Å2-0.0053 Å2-0.0424 Å20.0126 Å2--0.0382 Å2
L0.4998 °20.0849 °20.1674 °2-0.4653 °20.0202 °2--0.3971 °2
S0.0534 Å °0.0237 Å °-0.0072 Å °0.0415 Å °-0.0234 Å °0.0062 Å °0.0432 Å °0.0516 Å °-0.0244 Å °
Refinement TLS groupSelection details: ALL

+
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