[English] 日本語
Yorodumi
- PDB-1ogl: The crystal structure of native Trypanosoma cruzi dUTPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ogl
TitleThe crystal structure of native Trypanosoma cruzi dUTPase
ComponentsDEOXYURIDINE TRIPHOSPHATASEDUTP diphosphatase
KeywordsHYDROLASE / DUTPASE / TRYPANOSOMA CRUZI / NATIVE / DIMER
Function / homologyall-alpha NTP pyrophosphatase / Type II deoxyuridine triphosphatase / all-alpha NTP pyrophosphatases / Type II deoxyuridine triphosphatase / dUTPase/dCTP pyrophosphatase / dUTPase / Up-down Bundle / Mainly Alpha / Deoxyuridine triphosphatase
Function and homology information
Biological speciesTRYPANOSOMA CRUZI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsHarkiolaki, M. / Dodson, E.J. / Bernier-Villamor, V. / Turkenburg, J.P. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: Structure / Year: 2004
Title: The Crystal Structure of Trypanosoma Cruzi Dutpase Reveals a Novel Dutp/Dudp Binding Fold
Authors: Harkiolaki, M. / Dodson, E.J. / Bernier-Villamor, V. / Turkenburg, J.P. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionMay 7, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DEOXYURIDINE TRIPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)32,1041
Polymers32,1041
Non-polymers00
Water61334
1
A: DEOXYURIDINE TRIPHOSPHATASE

A: DEOXYURIDINE TRIPHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)64,2092
Polymers64,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)136.434, 136.434, 68.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

-
Components

#1: Protein DEOXYURIDINE TRIPHOSPHATASE / DUTP diphosphatase / DUTPASE


Mass: 32104.342 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TRYPANOSOMA CRUZI (eukaryote) / Strain: Y / Plasmid: PET-11C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15923, dUTP diphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.9 Å3/Da / Density % sol: 57 %
Description: ADDITIONAL PHASE INFORMATION PROVIDED THROUGH MERCURYL DERIVATIVE
Crystal growpH: 6.6
Details: 15% PEG 2000 MME, 0.1 M LISO4, 50 MM SODIUM CACODYLATE PH 6.6
Crystal grow
*PLUS
Temperature: 290 K / pH: 6.6 / Method: vapor diffusion, hanging drop / Details: Harkiolaki, M., (2001) Acta Cryst., D57, 915.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %PEG2000 MME1reservoir
20.10 M1reservoirLiSO4
350 mMsodium cacodylate1reservoirpH6.6
420 mg/mlprotein1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9688
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2000 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9688 Å / Relative weight: 1
ReflectionResolution: 2.4→12 Å / Num. obs: 14827 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 32.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 4.1 / % possible all: 88.4
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 12 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 88.4 % / Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 4.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
MLPHAREphasing
AMoREphasing
RefinementMethod to determine structure: MAD
Starting model: LOW RESOLUTION MAD STRUCTURE

Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.775 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 724 4.9 %RANDOM
Rwork0.203 ---
obs0.206 14099 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2003 0 0 34 2037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212047
X-RAY DIFFRACTIONr_bond_other_d0.0020.021853
X-RAY DIFFRACTIONr_angle_refined_deg1.5421.9412772
X-RAY DIFFRACTIONr_angle_other_deg0.90634299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4275243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022256
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02426
X-RAY DIFFRACTIONr_nbd_refined0.2130.2452
X-RAY DIFFRACTIONr_nbd_other0.2280.22090
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.21205
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2030.241
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2350.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8561.51224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64821969
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.3693823
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9314.5803
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.347 61
Rwork0.273 970
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 12 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_d0.030.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg2.122

+
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