[English] 日本語
Yorodumi
- PDB-7jt8: Apo structure of a pseudomurein peptide ligase type E from Methan... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jt8
TitleApo structure of a pseudomurein peptide ligase type E from Methanothermus fervidus
ComponentsMur ligase middle domain protein
KeywordsLIGASE / Pseudomurein / pseudomurein peptide ligase / archaeal cell wall / Methanothermus fervidus / pMurE
Function / homology
Function and homology information


acid-amino acid ligase activity / biosynthetic process / ATP binding
Similarity search - Function
Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / 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 ...Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Mur ligase middle domain protein
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsCarbone, V. / Schofield, L.R. / Sutherland-Smith, A.J. / Ronimus, R.S. / Subedi, B.P.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Royal Society of New ZealandAGR1301 New Zealand
CitationJournal: Microbiology (Reading, Engl.) / Year: 2022
Title: Structural characterisation of methanogen pseudomurein cell wall peptide ligases homologous to bacterial MurE/F murein peptide ligases.
Authors: Subedi, B.P. / Schofield, L.R. / Carbone, V. / Wolf, M. / Martin, W.F. / Ronimus, R.S. / Sutherland-Smith, A.J.
History
DepositionAug 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
I: Mur ligase middle domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6606
Polymers54,2511
Non-polymers4095
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-66 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.783, 119.783, 70.746
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

-
Components

#1: Protein Mur ligase middle domain protein / pseudomurein peptide ligase type E


Mass: 54251.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (strain ATCC 43054 / DSM 2088 / JCM 10308 / V24 S) (archaea)
Strain: ATCC 43054 / DSM 2088 / JCM 10308 / V24 S / Gene: Mfer_0762 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: E3GZ29, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: 0.2 M ammonium sulfate, 30% w/v PEG4000, pH 5.4

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.84→34.58 Å / Num. obs: 50277 / % possible obs: 99.85 % / Redundancy: 22.4 % / Biso Wilson estimate: 21.37 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.091 / Net I/σ(I): 29.3
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3066 / CC1/2: 0.91 / % possible all: 97.9

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
MrBUMPphasing
PHASERphasing
SHELXEmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4QDI

4qdi


Resolution: 1.84→34.58 Å / SU ML: 0.1876 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5106
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2111 2645 5.26 %
Rwork0.1751 47632 -
obs0.1771 50277 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.03 Å2
Refinement stepCycle: LAST / Resolution: 1.84→34.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3792 0 21 392 4205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663958
X-RAY DIFFRACTIONf_angle_d0.85835368
X-RAY DIFFRACTIONf_chiral_restr0.0576630
X-RAY DIFFRACTIONf_plane_restr0.0053672
X-RAY DIFFRACTIONf_dihedral_angle_d5.7208535
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.870.3011500.23832458X-RAY DIFFRACTION97.9
1.87-1.910.31681350.26162481X-RAY DIFFRACTION99.85
1.91-1.950.25971160.24342486X-RAY DIFFRACTION99.69
1.95-1.990.22081170.20192535X-RAY DIFFRACTION100
1.99-2.040.22981130.18912518X-RAY DIFFRACTION100
2.04-2.090.25161310.21272493X-RAY DIFFRACTION99.89
2.09-2.140.23491220.18542539X-RAY DIFFRACTION100
2.14-2.210.21321440.18542498X-RAY DIFFRACTION100
2.21-2.280.2231420.18752479X-RAY DIFFRACTION100
2.28-2.360.21951640.18562488X-RAY DIFFRACTION100
2.36-2.450.24871290.18312498X-RAY DIFFRACTION100
2.45-2.560.20461480.18112496X-RAY DIFFRACTION100
2.56-2.70.23541740.17462472X-RAY DIFFRACTION99.96
2.7-2.870.21751410.18032512X-RAY DIFFRACTION100
2.87-3.090.21231620.17792514X-RAY DIFFRACTION100
3.09-3.40.23841380.17372507X-RAY DIFFRACTION100
3.4-3.890.1821480.15422516X-RAY DIFFRACTION100
3.89-4.90.15761320.13862544X-RAY DIFFRACTION100
4.9-34.580.18011390.15772598X-RAY DIFFRACTION99.93

+
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