[English] 日本語
Yorodumi
- PDB-9g53: The structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphoryla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9g53
TitleThe structure of Aspergillus fumigatus UDP-GlcNAc pyrophosphorylase in complex with a fragment
Components(UDP-N-acetylglucosamine ...) x 2
KeywordsTRANSFERASE / Aspergillus / UAP1 / fragment
Function / homology
Function and homology information


UDP-N-acetylglucosamine diphosphorylase / UDP-N-acetylglucosamine diphosphorylase activity / UDP-N-acetylglucosamine biosynthetic process
Similarity search - Function
UDP-sugar pyrophosphorylase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
3-aminobenzonitrile / : / Chem-GN1 / UDP-N-acetylglucosamine diphosphorylase
Similarity search - Component
Biological speciesAspergillus fumigatus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYan, K.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/V001094/1 United Kingdom
CitationJournal: To Be Published
Title: Exploration of starting points for the chemical validation of UDP-N-acetylglucosamine pyrophosphorylase in Aspergillus fumigatus
Authors: Yan, K. / Stanley, M. / Raimi, O. / Kowalski, B. / Gurvic, D. / Grillenberger, S. / Chen, X. / Ferenbach, A.T. / Dorfmueller, H. / van Aalten, D.M.F.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: UDP-N-acetylglucosamine diphosphorylase
A: UDP-N-acetylglucosamine diphosphorylase
C: UDP-N-acetylglucosamine diphosphorylase
D: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,76613
Polymers215,4074
Non-polymers1,3599
Water9,260514
1
B: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4955
Polymers53,8801
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3533
Polymers53,8801
Non-polymers4722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8592
Polymers53,8231
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: UDP-N-acetylglucosamine diphosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0593
Polymers53,8231
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.670, 136.770, 142.550
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
UDP-N-acetylglucosamine ... , 2 types, 4 molecules BACD

#1: Protein UDP-N-acetylglucosamine diphosphorylase


Mass: 53880.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: KXV57_008857 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A229XUD0, UDP-N-acetylglucosamine diphosphorylase
#2: Protein UDP-N-acetylglucosamine diphosphorylase


Mass: 53823.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus (mold) / Gene: KXV57_008857 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A229XUD0, UDP-N-acetylglucosamine diphosphorylase

-
Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-GN1 / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucopyranose / 2-(ACETYLAMINO)-2-DEOXY-1-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE / N-ACETYL-D-GLUCOSAMINE-1-PHOSPHATE / N-acetyl-1-O-phosphono-alpha-D-glucosamine / 2-acetamido-2-deoxy-1-O-phosphono-alpha-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-D-glucose / 2-acetamido-2-deoxy-1-O-phosphono-glucose


Type: D-saccharide / Mass: 301.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H16NO9P
IdentifierTypeProgram
a-D-Glcp1PO3NAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

-
Non-polymers , 5 types, 521 molecules

#4: Chemical ChemComp-A1IIG / (3~{S})-3-azanyl-3-thiophen-2-yl-propanoic acid


Mass: 171.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9NO2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-71G / 3-aminobenzonitrile


Mass: 118.136 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H6N2
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 514 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium acetate 25 % PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.96→51.87 Å / Num. obs: 151726 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.998 / Net I/σ(I): 7.7
Reflection shellResolution: 1.96→1.99 Å / Num. unique obs: 7449 / CC1/2: 0.352

-
Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.96→48.5 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 7356 4.86 %
Rwork0.2162 --
obs0.2185 151479 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.96→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14510 0 89 514 15113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714950
X-RAY DIFFRACTIONf_angle_d0.83620214
X-RAY DIFFRACTIONf_dihedral_angle_d14.8495550
X-RAY DIFFRACTIONf_chiral_restr0.0522220
X-RAY DIFFRACTIONf_plane_restr0.0072647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.980.40392140.41074670X-RAY DIFFRACTION96
1.98-2.010.41342530.39434675X-RAY DIFFRACTION98
2.01-2.030.41592560.38034728X-RAY DIFFRACTION99
2.03-2.060.40822130.35724857X-RAY DIFFRACTION99
2.06-2.080.39122560.34244686X-RAY DIFFRACTION99
2.08-2.110.38912680.32574744X-RAY DIFFRACTION99
2.11-2.140.36833000.32354796X-RAY DIFFRACTION99
2.14-2.170.35632530.30384754X-RAY DIFFRACTION99
2.17-2.210.36672440.28854784X-RAY DIFFRACTION99
2.21-2.240.36552540.28344777X-RAY DIFFRACTION99
2.24-2.280.30052190.26754794X-RAY DIFFRACTION99
2.28-2.320.31962290.25894880X-RAY DIFFRACTION99
2.32-2.370.29852260.24324723X-RAY DIFFRACTION99
2.37-2.420.30432350.25134906X-RAY DIFFRACTION99
2.42-2.470.34092640.25814750X-RAY DIFFRACTION100
2.47-2.530.28192400.24564823X-RAY DIFFRACTION99
2.53-2.590.31242230.23294814X-RAY DIFFRACTION100
2.59-2.660.26272670.22754814X-RAY DIFFRACTION100
2.66-2.740.2882720.22134788X-RAY DIFFRACTION100
2.74-2.830.26281670.22734876X-RAY DIFFRACTION100
2.83-2.930.28822380.24344867X-RAY DIFFRACTION100
2.93-3.040.2933080.2354741X-RAY DIFFRACTION100
3.04-3.180.29762540.22954821X-RAY DIFFRACTION100
3.18-3.350.29791850.22694921X-RAY DIFFRACTION100
3.35-3.560.27142690.21464799X-RAY DIFFRACTION100
3.56-3.840.23562990.19284790X-RAY DIFFRACTION100
3.84-4.220.22292460.17144847X-RAY DIFFRACTION100
4.22-4.830.19912360.15064852X-RAY DIFFRACTION100
4.83-6.090.20412270.17114918X-RAY DIFFRACTION100
6.09-48.50.17482410.1654928X-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