[English] 日本語
Yorodumi
- PDB-8f73: Crystal structure of Pseudomonas aeruginosa UDP-glucose phosphory... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f73
TitleCrystal structure of Pseudomonas aeruginosa UDP-glucose phosphorylase in complex with UDP-glucose
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / UGP / UDP-Glucose pyrophosphorylase / UTP:glucose-1-phosphate uridylyltransferase
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-alpha-D-glucose metabolic process / lipopolysaccharide core region biosynthetic process
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
ACETATE ION / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsDirr, L. / Fuehring, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1157150 Australia
CitationJournal: Mbio / Year: 2024
Title: Tetramerization is essential for the enzymatic function of the Pseudomonas aeruginosa virulence factor UDP-glucose pyrophosphorylase.
Authors: Dirr, L. / Cleeves, S. / Ramon Roth, I. / Li, L. / Fiebig, T. / Ve, T. / Haussler, S. / Braun, A. / von Itzstein, M. / Fuhring, J.I.
History
DepositionNov 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase
E: UTP--glucose-1-phosphate uridylyltransferase
F: UTP--glucose-1-phosphate uridylyltransferase
G: UTP--glucose-1-phosphate uridylyltransferase
H: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,56828
Polymers254,5978
Non-polymers4,97020
Water1,838102
1
A: UTP--glucose-1-phosphate uridylyltransferase
H: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

B: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

F: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,78214
Polymers127,2994
Non-polymers2,48410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area15860 Å2
ΔGint-111 kcal/mol
Surface area41580 Å2
MethodPISA
2
C: UTP--glucose-1-phosphate uridylyltransferase
G: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules

D: UTP--glucose-1-phosphate uridylyltransferase
E: UTP--glucose-1-phosphate uridylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,78514
Polymers127,2994
Non-polymers2,48710
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area15870 Å2
ΔGint-105 kcal/mol
Surface area41640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.715, 114.847, 155.761
Angle α, β, γ (deg.)90.000, 97.390, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
UTP--glucose-1-phosphate uridylyltransferase / Alpha-D-glucosyl-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / Uridine ...Alpha-D-glucosyl-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / Uridine diphosphoglucose pyrophosphorylase


Mass: 31824.680 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: galU, PA2023 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9I291, UTP-glucose-1-phosphate uridylyltransferase

-
Non-polymers , 5 types, 122 molecules

#2: Chemical
ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate trihydrate pH 4.6 2.0 M sodium formate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953722 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953722 Å / Relative weight: 1
ReflectionResolution: 2.9→48.52 Å / Num. obs: 65768 / % possible obs: 99.7 % / Redundancy: 3.9 % / Biso Wilson estimate: 60.43 Å2 / CC1/2: 0.96 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.3
Reflection shellResolution: 2.9→2.97 Å / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4608 / CC1/2: 1 / Rpim(I) all: 0.58

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JUK

3juk


Resolution: 2.9→46.98 Å / SU ML: 0.3435 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2357 3227 4.93 %
Rwork0.1948 62216 -
obs0.1968 65443 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.16 Å2
Refinement stepCycle: LAST / Resolution: 2.9→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17256 0 312 102 17670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007317881
X-RAY DIFFRACTIONf_angle_d0.996924178
X-RAY DIFFRACTIONf_chiral_restr0.05882736
X-RAY DIFFRACTIONf_plane_restr0.0053096
X-RAY DIFFRACTIONf_dihedral_angle_d16.44766930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.940.33181490.29192704X-RAY DIFFRACTION99.55
2.94-2.990.3151490.29482660X-RAY DIFFRACTION99.75
2.99-3.040.32531470.27522691X-RAY DIFFRACTION99.44
3.04-3.090.33981370.26612687X-RAY DIFFRACTION99.47
3.09-3.150.28751360.25432685X-RAY DIFFRACTION99.61
3.15-3.210.29421320.25192678X-RAY DIFFRACTION99.12
3.21-3.270.31461250.24792737X-RAY DIFFRACTION99.44
3.27-3.340.30581520.23912652X-RAY DIFFRACTION99.19
3.34-3.420.2721390.23532713X-RAY DIFFRACTION99.58
3.42-3.510.26161280.21172695X-RAY DIFFRACTION99.82
3.51-3.60.27511440.19922697X-RAY DIFFRACTION99.79
3.6-3.710.25121430.18722714X-RAY DIFFRACTION99.58
3.71-3.830.21291470.18772696X-RAY DIFFRACTION99.82
3.83-3.960.22441520.18372685X-RAY DIFFRACTION99.75
3.96-4.120.26441380.18162702X-RAY DIFFRACTION99.75
4.12-4.310.19541370.16792734X-RAY DIFFRACTION99.86
4.31-4.540.20631290.15252703X-RAY DIFFRACTION99.65
4.54-4.820.20171360.14642718X-RAY DIFFRACTION99.86
4.82-5.190.18081400.15412738X-RAY DIFFRACTION99.69
5.19-5.720.19321400.17892724X-RAY DIFFRACTION99.69
5.72-6.540.23751440.21132723X-RAY DIFFRACTION99.76
6.54-8.230.22291570.20132713X-RAY DIFFRACTION99.41
8.23-46.980.18811260.17642767X-RAY DIFFRACTION97.8

+
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