[English] 日本語
Yorodumi
- PDB-7bpd: Crystal structural analysis of Swine dUTPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7bpd
TitleCrystal structural analysis of Swine dUTPase
ComponentsDeoxyuridine triphosphatase
KeywordsHYDROLASE / SWINE / dUTPASE / sDUT
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 / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily
Similarity search - Domain/homology
Deoxyuridine 5'-triphosphate nucleotidohydrolase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsLiang, R. / Peng, G.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31722056 China
CitationJournal: To Be Published
Title: Crystal structural analysis of swine dUTPase
Authors: Liang, R. / Peng, G.Q.
History
DepositionMar 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Deoxyuridine triphosphatase
B: Deoxyuridine triphosphatase


Theoretical massNumber of molelcules
Total (without water)37,0742
Polymers37,0742
Non-polymers00
Water3,621201
1
A: Deoxyuridine triphosphatase
B: Deoxyuridine triphosphatase

A: Deoxyuridine triphosphatase


Theoretical massNumber of molelcules
Total (without water)55,6113
Polymers55,6113
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)116.175, 54.535, 52.107
Angle α, β, γ (deg.)90.000, 116.680, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Deoxyuridine triphosphatase


Mass: 18537.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: DUT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A4X1SHL3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.99 Å3/Da / Density % sol: 38.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 200mM NaI, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97835 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97835 Å / Relative weight: 1
ReflectionResolution: 2.03→51.9 Å / Num. obs: 35796 / % possible obs: 83 % / Redundancy: 5.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.029 / Rrim(I) all: 0.074 / Χ2: 0.968 / Net I/σ(I): 23.67
Reflection shellResolution: 2.04→2.08 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 2 / Num. unique obs: 1301 / CC1/2: 0.972 / CC star: 0.993 / Rpim(I) all: 0.378 / Rrim(I) all: 0.968

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HQU

2hqu


Resolution: 2.04→46.62 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.9 / SU B: 5.063 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 737 4.8 %RANDOM
Rwork0.2073 ---
obs0.21 14516 80.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 149.4 Å2 / Biso mean: 38.493 Å2 / Biso min: 0.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å20.08 Å2
2---0.34 Å2-0 Å2
3---0.11 Å2
Refinement stepCycle: final / Resolution: 2.04→46.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 0 201 2273
Biso mean---38.88 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132112
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171998
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.6492848
X-RAY DIFFRACTIONr_angle_other_deg1.2181.5844610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0615262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.95720.984122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.69915364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4111520
X-RAY DIFFRACTIONr_chiral_restr0.0620.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02476
LS refinement shellResolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 24 -
Rwork0.2 664 -
all-688 -
obs--48.55 %

+
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