[English] 日本語
Yorodumi
- PDB-9dr4: Crystal structure of bifunctional GlmU from Staphylococcus aureus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9dr4
TitleCrystal structure of bifunctional GlmU from Staphylococcus aureus NCTC 8325 complexed with UTP, CoA and Glc 1-P
ComponentsBifunctional protein GlmU
KeywordsTRANSFERASE / uridyltransferase / acetyltransferase
Function / homology
Function and homology information


glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape ...glucosamine-1-phosphate N-acetyltransferase / glucosamine-1-phosphate N-acetyltransferase activity / UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process / lipid A biosynthetic process / peptidoglycan biosynthetic process / cell wall organization / cell morphogenesis / regulation of cell shape / magnesium ion binding / membrane / cytoplasm
Similarity search - Function
Bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase / GlmU, C-terminal LbH domain / : / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Nucleotidyl transferase domain / Nucleotidyl transferase / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
COENZYME A / 1-O-phosphono-alpha-D-glucopyranose / URIDINE 5'-TRIPHOSPHATE / Bifunctional protein GlmU
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsPederick, J.L. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Protein Sci. / Year: 2025
Title: Functional and structural characterization of Staphylococcus aureus N-acetylglucosamine 1-phosphate uridyltransferase (GlmU) reveals a redox-sensitive acetyltransferase activity.
Authors: Pederick, J.L. / Kumar, A. / Pukala, T.L. / Bruning, J.B.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2595
Polymers49,7231
Non-polymers1,5364
Water4,720262
1
A: Bifunctional protein GlmU
hetero molecules

A: Bifunctional protein GlmU
hetero molecules

A: Bifunctional protein GlmU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,77715
Polymers149,1683
Non-polymers4,60812
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area18940 Å2
ΔGint-60 kcal/mol
Surface area48430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.883, 94.883, 262.532
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-216-

ARG

21A-502-

MG

31A-612-

HOH

41A-824-

HOH

51A-830-

HOH

61A-849-

HOH

71A-853-

HOH

81A-854-

HOH

-
Components

-
Protein / Sugars , 2 types, 2 molecules A

#1: Protein Bifunctional protein GlmU


Mass: 49722.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus NCTC 8325 (bacteria)
Gene: glmU, SAOUHSC_00471 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q2G0S3, UDP-N-acetylglucosamine diphosphorylase, glucosamine-1-phosphate N-acetyltransferase
#4: Sugar ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 4 types, 265 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C9H15N2O15P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: UTP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.22 % / Description: Trapezoid
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2M lithium citrate tribasic tetrahydrate, 15 - 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→39.21 Å / Num. obs: 39284 / % possible obs: 100 % / Redundancy: 20.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.239 / Rpim(I) all: 0.054 / Rrim(I) all: 0.245 / Χ2: 0.99 / Net I/σ(I): 12.1 / Num. measured all: 796494
Reflection shellResolution: 1.85→1.89 Å / % possible obs: 100 % / Redundancy: 20.4 % / Rmerge(I) obs: 3.603 / Num. measured all: 49237 / Num. unique obs: 2410 / CC1/2: 0.526 / Rpim(I) all: 0.814 / Rrim(I) all: 3.695 / Χ2: 0.95 / Net I/σ(I) obs: 1.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.15data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→39.21 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2128 1996 5.09 %
Rwork0.1748 --
obs0.1767 39244 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→39.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 92 262 3673
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093489
X-RAY DIFFRACTIONf_angle_d1.0244764
X-RAY DIFFRACTIONf_dihedral_angle_d14.131232
X-RAY DIFFRACTIONf_chiral_restr0.068568
X-RAY DIFFRACTIONf_plane_restr0.009616
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.32741400.28752628X-RAY DIFFRACTION100
1.9-1.950.27571610.25472623X-RAY DIFFRACTION100
1.95-20.29081430.22832607X-RAY DIFFRACTION100
2-2.070.26891470.20982643X-RAY DIFFRACTION100
2.07-2.140.23061550.19322611X-RAY DIFFRACTION100
2.14-2.230.241270.17992661X-RAY DIFFRACTION100
2.23-2.330.22211170.17292656X-RAY DIFFRACTION100
2.33-2.450.22771520.16962644X-RAY DIFFRACTION100
2.45-2.610.23641470.17482623X-RAY DIFFRACTION100
2.61-2.810.2291260.17352697X-RAY DIFFRACTION100
2.81-3.090.19681520.17112639X-RAY DIFFRACTION100
3.09-3.540.22381290.16652700X-RAY DIFFRACTION100
3.54-4.460.16061500.14442710X-RAY DIFFRACTION100
4.46-39.210.18791500.16452806X-RAY DIFFRACTION99

+
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