[English] 日本語
Yorodumi
- PDB-4dl8: Crystal structure of Trypanosoma brucei dUTPase with dUMP, planar... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dl8
TitleCrystal structure of Trypanosoma brucei dUTPase with dUMP, planar [AlF3-OPO3] transition state analogue, Mg2+, and Na+
ComponentsDeoxyuridine triphosphataseDUTP diphosphatase
KeywordsHYDROLASE / all alpha NTP pyrophosphohydrolase / all alpha NTP pyrophosphatase
Function / homology
Function and homology information


dUTP diphosphatase / dUTP diphosphatase activity / nucleoplasm / metal ion binding
Similarity search - Function
Type II deoxyuridine triphosphatase / all-alpha NTP pyrophosphatase fold / dUTPase/dCTP pyrophosphatase / dUTPase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ALUMINUM FLUORIDE / PHOSPHATE ION / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / Deoxyuridine triphosphatase, putative
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / REFINED 4DKB / Resolution: 1.698 Å
AuthorsHemsworth, G.R. / Gonzalez-Pacanowska, D. / Wilson, K.S.
CitationJournal: Biochem.J. / Year: 2013
Title: On the catalytic mechanism of dimeric dUTPases.
Authors: Hemsworth, G.R. / Gonzalez-Pacanowska, D. / Wilson, K.S.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7637
Polymers32,2041
Non-polymers5596
Water2,990166
1
A: Deoxyuridine triphosphatase
hetero molecules

A: Deoxyuridine triphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,52614
Polymers64,4092
Non-polymers1,11712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area5830 Å2
ΔGint-106 kcal/mol
Surface area18850 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)68.590, 68.590, 123.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Deoxyuridine triphosphatase / DUTP diphosphatase / deoxyuridine triphosphate nucleotidohydrolase


Mass: 32204.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Strain: 427 / Gene: Tb927.7.5160 / Plasmid: pET-YSBLLIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57ZH3, dUTP diphosphatase

-
Non-polymers , 6 types, 172 molecules

#2: Chemical ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP / Deoxyuridine monophosphate


Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.26 Å3/Da / Density % sol: 45.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium sulfate, 0.1 M Bis-Tris propane, pH 6.5, 20% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.917 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 28, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.698→28.203 Å / Num. all: 33398 / Num. obs: 33398 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 15.7 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 23.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.698-1.7915.70.9230.87417947100.92398.4
1.79-1.9150.5861.36810045350.586100
1.9-2.03160.3612.16873242870.361100
2.03-2.1916.70.213.76672040010.21100
2.19-2.416.30.145.46037736970.14100
2.4-2.6815.20.0957.85117233630.095100
2.68-3.115.70.06211.44702629880.062100
3.1-3.816.20.04215.34165725670.042100
3.8-5.3714.40.03218.82933320400.03299.9
5.37-29.77315.10.0315.61830212100.0399.4

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
REFMAC5.5.0109phasing
RefinementMethod to determine structure: REFINED 4DKB
Starting model: PDB ENTRY 4DKB
Resolution: 1.698→28.2 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1759 / WRfactor Rwork: 0.1545 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8909 / SU B: 1.681 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0828 / SU Rfree: 0.0837 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 1661 5 %RANDOM
Rwork0.1667 ---
all0.1681 33398 --
obs0.1681 33293 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 424.2 Å2 / Biso mean: 25.9297 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1.01 Å2
Refinement stepCycle: LAST / Resolution: 1.698→28.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 32 166 1962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0271836
X-RAY DIFFRACTIONr_bond_other_d0.0010.021184
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9922493
X-RAY DIFFRACTIONr_angle_other_deg0.94432893
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1065222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52724.88184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.82515297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.339158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02360
X-RAY DIFFRACTIONr_mcbond_it20.911.51114
X-RAY DIFFRACTIONr_mcbond_other0.6061.5452
X-RAY DIFFRACTIONr_mcangle_it18.15521785
X-RAY DIFFRACTIONr_scbond_it21.2863722
X-RAY DIFFRACTIONr_scangle_it17.6054.5708
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 121 -
Rwork0.263 2237 -
all-2358 -
obs--97.44 %

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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