[English] 日本語
Yorodumi
- PDB-9bn8: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate lig... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9bn8
TitleCrystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19
ComponentsUDP-N-acetylmuramoylalanine--D-glutamate ligase
KeywordsLIGASE/LIGASE INHIBITOR / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / MurD / LIGASE / LIGASE-LIGASE INHIBITOR complex
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase / UDP-N-acetylmuramoylalanine-D-glutamate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
Mur ligase MurD-like, N-terminal domain / UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase, C-terminal / Mur ligase, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain
Similarity search - Domain/homology
: / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE / UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal Structure of UDP-N-acetylmuramoylalanine--D-glutamate ligase (MurD) from E. coli in complex with UMA and inhibitor A19
Authors: Liu, L. / Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionMay 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-N-acetylmuramoylalanine--D-glutamate ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,10615
Polymers47,9061
Non-polymers2,20014
Water9,080504
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.488, 65.488, 134.764
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein UDP-N-acetylmuramoylalanine--D-glutamate ligase


Mass: 47906.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: murD / Plasmid: EscoA.17938.a.AE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P14900

-
Non-polymers , 5 types, 518 molecules

#2: Chemical ChemComp-UMA / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE


Type: L-peptide linking / Mass: 750.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H36N4O20P2
#3: Chemical ChemComp-A1AQS / N-(4-{[(4S)-3-amino[1,2,4]triazolo[4,3-b]pyridazin-6-yl]sulfanyl}phenyl)acetamide


Mass: 300.339 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N6OS / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the ...Details: 1.9M ammonium sulfate, 7% (v/v) PEG 400, 0.1M Hepes 7.5. EscoA.17938.a.AE1.PW39153 at 17.4 mg/mL. Soaked with 2mM A19 in crystallant (10 ul) for 2h, and transferred to another 10 ul of the same solution for another 2h. plate Liu-Lim-116 A2. Puck: PSL-0401, Cryo: 2.5M Lithium Sulfate + 2mM inhibitor A19

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 13, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.35→67.38 Å / Num. obs: 124023 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.019 / Rrim(I) all: 0.072 / Χ2: 0.99 / Net I/σ(I): 17.7 / Num. measured all: 1676743
Reflection shellResolution: 1.35→1.39 Å / % possible obs: 100 % / Redundancy: 10 % / Rmerge(I) obs: 1.317 / Num. measured all: 91897 / Num. unique obs: 9171 / CC1/2: 0.682 / Rpim(I) all: 0.435 / Rrim(I) all: 1.388 / Χ2: 1.01 / Net I/σ(I) obs: 1.8

-
Processing

Software
NameVersionClassification
PHENIX(dev_5318: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→58.9 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1575 6027 4.86 %
Rwork0.1327 --
obs0.1339 123930 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.35→58.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3260 0 131 504 3895
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073577
X-RAY DIFFRACTIONf_angle_d0.9194895
X-RAY DIFFRACTIONf_dihedral_angle_d12.3791285
X-RAY DIFFRACTIONf_chiral_restr0.079560
X-RAY DIFFRACTIONf_plane_restr0.011633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.35-1.370.24012470.21673946X-RAY DIFFRACTION100
1.37-1.380.22772280.20453856X-RAY DIFFRACTION100
1.38-1.40.22251490.19383962X-RAY DIFFRACTION100
1.4-1.420.21251950.18313932X-RAY DIFFRACTION100
1.42-1.430.24841910.19713911X-RAY DIFFRACTION100
1.43-1.450.22482090.18633943X-RAY DIFFRACTION100
1.45-1.480.19281990.16643897X-RAY DIFFRACTION100
1.48-1.50.21191690.14883968X-RAY DIFFRACTION100
1.5-1.520.17262000.13323918X-RAY DIFFRACTION100
1.52-1.550.1461940.12223949X-RAY DIFFRACTION100
1.55-1.570.1392230.11283873X-RAY DIFFRACTION100
1.57-1.60.14111860.10863945X-RAY DIFFRACTION100
1.6-1.630.14041850.1123951X-RAY DIFFRACTION100
1.63-1.660.15551630.1153932X-RAY DIFFRACTION100
1.66-1.70.1552080.12043921X-RAY DIFFRACTION100
1.7-1.740.13652010.12633946X-RAY DIFFRACTION100
1.74-1.780.15392170.13183880X-RAY DIFFRACTION100
1.78-1.830.16661890.14133946X-RAY DIFFRACTION100
1.83-1.890.14711880.13013950X-RAY DIFFRACTION100
1.89-1.950.14721930.12123927X-RAY DIFFRACTION100
1.95-2.020.14112350.12033885X-RAY DIFFRACTION100
2.02-2.10.14932150.11513947X-RAY DIFFRACTION100
2.1-2.190.14782150.11663903X-RAY DIFFRACTION100
2.19-2.310.1412190.11873910X-RAY DIFFRACTION100
2.31-2.450.13561750.11533964X-RAY DIFFRACTION100
2.45-2.640.16082120.12623935X-RAY DIFFRACTION100
2.64-2.910.15741860.14033945X-RAY DIFFRACTION100
2.91-3.330.17032280.14223923X-RAY DIFFRACTION100
3.33-4.190.1392060.12573961X-RAY DIFFRACTION100
4.2-58.90.1692020.14633977X-RAY DIFFRACTION100

+
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