[English] 日本語
Yorodumi
- PDB-3h6x: Crystal structure of dUTPase from Streptococcus mutans -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h6x
TitleCrystal structure of dUTPase from Streptococcus mutans
ComponentsdUTPase
KeywordsHYDROLASE / jelly-roll beta-barrel
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / magnesium ion binding
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
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLi, G.L. / Wang, K.T. / Liu, X. / Li, L.F. / Su, X.D.
CitationJournal: To be Published
Title: Structure and activity analysis of dUTP nucleotidohydrolase from Streptococcus mutans
Authors: Li, G.L. / Wang, K.T. / Liu, X. / Li, L.F. / Su, X.D.
History
DepositionApr 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dUTPase
B: dUTPase
C: dUTPase


Theoretical massNumber of molelcules
Total (without water)49,1753
Polymers49,1753
Non-polymers00
Water12,394688
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-42 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.780, 53.520, 93.140
Angle α, β, γ (deg.)90.00, 113.91, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-420-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 4:132 )A4 - 132
211chain B and (resseq 4:132 )B4 - 132
311chain C and (resseq 4:132 )C4 - 132

-
Components

#1: Protein dUTPase


Mass: 16391.641 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: dut / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DVY3, dUTP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 688 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2, 25% polyethylene glycol(PEG)3350, 0.1M Tris-HCl(pH 8.5), pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.9787 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 43830 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 11.33 Å2 / Rsym value: 0.047 / Net I/σ(I): 15.25
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 8.97 / Num. unique all: 7142 / Rsym value: 0.123 / % possible all: 96.1

-
Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→19.941 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.7 / FOM work R set: 0.885 / SU B: 1.831 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.09 / Phase error: 18.8 / Stereochemistry target values: MLHL / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2051 1994 4.62 %RANDOM
Rwork0.1833 41170 --
obs0.1843 43164 97.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.132 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 50.15 Å2 / Biso mean: 14.753 Å2 / Biso min: 1.54 Å2
Baniso -1Baniso -2Baniso -3
1--1.128 Å20 Å2-1.201 Å2
2---0.474 Å2-0 Å2
3---1.602 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 0 688 3696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093059
X-RAY DIFFRACTIONf_angle_d1.2594144
X-RAY DIFFRACTIONf_dihedral_angle_d16.0861113
X-RAY DIFFRACTIONf_chiral_restr0.112473
X-RAY DIFFRACTIONf_plane_restr0.006543
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1002X-RAY DIFFRACTIONPOSITIONAL0.072
12B1002X-RAY DIFFRACTIONPOSITIONAL0.072
13C995X-RAY DIFFRACTIONPOSITIONAL0.053
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.74250.231210.19482577X-RAY DIFFRACTION86
1.7425-1.78960.21471550.17542928X-RAY DIFFRACTION98
1.7896-1.84220.22361420.17912911X-RAY DIFFRACTION98
1.8422-1.90160.2031320.1812939X-RAY DIFFRACTION98
1.9016-1.96950.2051420.18252924X-RAY DIFFRACTION99
1.9695-2.04830.2341480.17712975X-RAY DIFFRACTION99
2.0483-2.14140.19621430.17642979X-RAY DIFFRACTION99
2.1414-2.25420.19361420.19062976X-RAY DIFFRACTION99
2.2542-2.39520.211430.19272940X-RAY DIFFRACTION99
2.3952-2.57980.2041470.18472990X-RAY DIFFRACTION99
2.5798-2.83870.23631360.19723007X-RAY DIFFRACTION99
2.8387-3.2480.18731570.1822991X-RAY DIFFRACTION99
3.248-4.08630.181420.16343007X-RAY DIFFRACTION99
4.0863-19.94240.18641440.16933026X-RAY DIFFRACTION97

+
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