[English] 日本語
Yorodumi
- PDB-1e0d: UDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e0d
TitleUDP-N-Acetylmuramoyl-L-Alanine:D-Glutamate Ligase
ComponentsUDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / MURD / ADP-FORMING ENZYME
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 domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain ...Mur ligase MurD-like, N-terminal domain / UDP-N-acetylmuramoylalanine-D-glutamate ligase MurD / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / NAD(P)-binding Rossmann-like Domain / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
UDP-N-acetylmuramoylalanine--D-glutamate ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFanchon, E. / Bertrand, J. / Chantalat, L. / Dideberg, O.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: "Open" Structures of Murd: Domain Movements and Structural Similarities with Folylpolyglutamate Synthetase.
Authors: Bertrand, J. / Fanchon, E. / Martin, L. / Chantalat, L. / Auger, G. / Blanot, D. / Van Heijenoort, J. / Dideberg, O.
History
DepositionMar 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 9, 2000Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jun 13, 2018Group: Advisory / Data collection / Structure summary
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / struct
Item: _diffrn_source.pdbx_synchrotron_beamline / _struct.title
Revision 1.3Dec 6, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
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)46,9852
Polymers46,8891
Non-polymers961
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.160, 69.160, 196.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE / MURD


Mass: 46889.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: JM83 (PMLD58)URCE / Gene: MURD GENE / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM83 (PMLD58)URCE
References: UniProt: P14900, UDP-N-acetylmuramoyl-L-alanine-D-glutamate ligase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growpH: 6 / Details: pH 6.00
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
19.8 mg/mlprotein1drop
21 mM1dropNaN3
31 mMdithiothreitol1drop
420 mMHEPES1drop
51.5-1.7 Mammonium sulfate1reservoir
6100 mMMES1reservoir
75 %(v/v)MPD1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: D2AM / Wavelength: 0.9801
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 23, 1997 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 19294 / % possible obs: 99 % / Redundancy: 7.3 % / Biso Wilson estimate: 25.5 Å2 / Rsym value: 0.04 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.8 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.21 / % possible all: 99.9
Reflection
*PLUS
% possible obs: 98.9 % / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.212

-
Processing

Software
NameVersionClassification
CNS0.4refinement
XDSdata reduction
CNS0.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2 DOMAINS FROM 1UAG

1uag


Resolution: 2.4→20 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 1911015.04 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY. RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON ...Details: RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY. RESIDUES 183-188 AND 221 - 222 WERE NOT VISIBLE IN THE ELECTRON DENSITY AND THEIR COORDINATES ARE NOT INCLUDED IN THIS ENTRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 781 4.9 %RANDOM
Rwork0.213 ---
obs0.213 15985 82 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.2219 Å2 / ksol: 0.365383 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.89 Å20 Å20 Å2
2--3.89 Å20 Å2
3----7.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3215 0 5 229 3449
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.752.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 93 5 %
Rwork0.246 1765 -
obs--58.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 40.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

+
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