[English] 日本語
Yorodumi
- PDB-3dmp: 2.6 A crystal structure of uracil phosphoribosyltransferase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dmp
Title2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei
ComponentsUracil phosphoribosyltransferase
KeywordsTRANSFERASE / BURKHOLDERIA / PSEUDOMALLEI / URACIL / PHOSPHORIBOSYLTRANSFERASE / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / Glycosyltransferase / Magnesium
Function / homology
Function and homology information


uracil salvage / uracil phosphoribosyltransferase / uracil phosphoribosyltransferase activity / UMP salvage / GTP binding / magnesium ion binding
Similarity search - Function
Uracil phosphoribosyltransferase, bacterial-type / Uracil phosphoribosyl transferase / Uracil phosphoribosyltransferase / : / Rossmann fold - #2020 / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil phosphoribosyltransferase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionJul 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)96,7884
Polymers96,7884
Non-polymers00
Water1,49583
1
A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase

A: Uracil phosphoribosyltransferase
B: Uracil phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)96,7884
Polymers96,7884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area12390 Å2
ΔGint-59 kcal/mol
Surface area31930 Å2
MethodPISA
2
C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase

C: Uracil phosphoribosyltransferase
D: Uracil phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)96,7884
Polymers96,7884
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area12520 Å2
ΔGint-65 kcal/mol
Surface area32250 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.222, 80.637, 141.833
Angle α, β, γ (deg.)90.00, 99.11, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Uracil phosphoribosyltransferase / UMP pyrophosphorylase / UPRTase


Mass: 24197.080 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: upp, BPSL1166 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q63VS8, uracil phosphoribosyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.98 Å3/Da / Density % sol: 58.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 2M NaCl, 5% PEG 4000, 0.1M TRIS, pH 8.5, VAPOR DIFFUSION, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 39360 / % possible obs: 99.7 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.155 / Net I/σ(I): 4.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obs% possible all
2.5-2.593.70.764100
2.59-2.693.80.663100
2.69-2.823.80.524100
2.82-2.963.80.402100
2.96-3.153.80.30899.9
3.15-3.393.80.21699.7
3.39-3.733.70.15899.5
3.73-4.273.70.12899.3
4.27-5.383.60.10299.1
5.38-503.70.08199.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 60.03 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å49.32 Å
Translation3 Å49.32 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→49.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.921 / Occupancy max: 1 / Occupancy min: 1 / SU B: 11.445 / SU ML: 0.242 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27053 1758 5 %RANDOM
Rwork0.21882 ---
obs0.22145 33305 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.02 Å2
2--0 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6694 0 0 83 6777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226832
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.999274
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7135850
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85322.441295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.261151175
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7641568
X-RAY DIFFRACTIONr_chiral_restr0.0950.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025122
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.22971
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24534
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.2201
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5811.54359
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02726917
X-RAY DIFFRACTIONr_scbond_it1.36332679
X-RAY DIFFRACTIONr_scangle_it2.34.52357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 126 -
Rwork0.311 2412 -
obs--99.88 %

+
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