[English] 日本語
Yorodumi
- PDB-9aux: Crystal structure of A. baumannii GuaB dCBS with inhibitor GNE2011 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9aux
TitleCrystal structure of A. baumannii GuaB dCBS with inhibitor GNE2011
ComponentsInosine-5'-monophosphate dehydrogenase
KeywordsOXIDOREDUCTASE / GuaB / IMPDH / inhibitor
Function / homology
Function and homology information


IMP dehydrogenase / IMP dehydrogenase activity / GMP biosynthetic process / GTP biosynthetic process / nucleotide binding / metal ion binding
Similarity search - Function
IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / INOSINIC ACID / Inosine-5'-monophosphate dehydrogenase / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsHarris, S.F. / Wu, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mbio / Year: 2024
Title: Discovery of GuaB inhibitors with efficacy against Acinetobacter baumannii infection.
Authors: Kofoed, E.M. / Aliagas, I. / Crawford, T. / Mao, J. / Harris, S.F. / Xu, M. / Wang, S. / Wu, P. / Ma, F. / Clark, K. / Sims, J. / Xu, Y. / Peng, Y. / Skippington, E. / Yang, Y. / Reeder, J. ...Authors: Kofoed, E.M. / Aliagas, I. / Crawford, T. / Mao, J. / Harris, S.F. / Xu, M. / Wang, S. / Wu, P. / Ma, F. / Clark, K. / Sims, J. / Xu, Y. / Peng, Y. / Skippington, E. / Yang, Y. / Reeder, J. / Ubhayakar, S. / Baumgardner, M. / Yan, Z. / Chen, J. / Park, S. / Zhang, H. / Yen, C.-W. / Lorenzo, M. / Skelton, N. / Liang, X. / Chen, L. / Hoag, B. / Li, C.S. / Liu, Z. / Wai, J. / Liu, X. / Liang, J. / Tan, M.W.
History
DepositionMar 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,22024
Polymers332,1798
Non-polymers6,04116
Water13,331740
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.689, 126.412, 126.387
Angle α, β, γ (deg.)90.00, 101.32, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


Mass: 41522.379 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: guaB, guaB, guaB_1, guaB_2 / Production host: Escherichia coli (E. coli)
References: UniProt: P31002, UniProt: A0A059ZJE9, IMP dehydrogenase
#2: Chemical
ChemComp-IMP / INOSINIC ACID


Mass: 348.206 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N4O8P
#3: Chemical
ChemComp-A1AG0 / 9-{(1R)-1-[(5P)-5-(4-chloro-1H-imidazol-2-yl)pyridin-3-yl]ethoxy}-1,4-dihydro-2H-pyrano[3,4-c]quinoline


Mass: 406.865 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C22H19ClN4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 740 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M Hepes, pH 7.5, 20% isopropanol, 10% PEG4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.45→123.93 Å / Num. obs: 234361 / % possible obs: 98.6 % / Redundancy: 3.4 % / CC1/2: 0.942 / Rmerge(I) obs: 0.234 / Rpim(I) all: 0.15 / Rrim(I) all: 0.279 / Net I/σ(I): 7.2
Reflection shellResolution: 2.45→2.59 Å / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.778 / Num. measured all: 64455 / Num. unique obs: 18344 / CC1/2: 0.642 / Rpim(I) all: 0.491 / Rrim(I) all: 0.923 / Net I/σ(I) obs: 3.2

-
Processing

Software
NameVersionClassification
PHENIX1.12-2829_finalrefinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.46→123.928 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0.44 / Phase error: 27.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 12003 5.12 %
Rwork0.1968 --
obs0.1995 234361 94.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.46→123.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19566 0 416 741 20723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720572
X-RAY DIFFRACTIONf_angle_d0.89727900
X-RAY DIFFRACTIONf_dihedral_angle_d17.08612242
X-RAY DIFFRACTIONf_chiral_restr0.0543230
X-RAY DIFFRACTIONf_plane_restr0.0053707

+
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