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- PDB-6vr8: Structure of a pseudomurein peptide ligase type E from Methanothe... -

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Basic information

Entry
Database: PDB / ID: 6vr8
TitleStructure 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 / Mur ligase family, 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
PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE / Mur ligase middle domain protein
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionFeb 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
I: Mur ligase middle domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1879
Polymers54,2511
Non-polymers9368
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-50 kcal/mol
Surface area20710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.369, 119.369, 71.088
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

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Components

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Protein , 1 types, 1 molecules I

#1: Protein Mur ligase middle domain protein / Pseudomurein peptide ligase type C


Mass: 54251.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Gene: Mfer_0762 / Plasmid: pET15b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 STAR
References: UniProt: E3GZ29, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Non-polymers , 6 types, 410 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 / Details: 0.2 M ammonium sulfate, 30% w/v PEG4000

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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
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→41.8 Å / Num. obs: 45561 / % possible obs: 100 % / Redundancy: 22 % / Biso Wilson estimate: 21.36 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.6
Reflection shellResolution: 1.94→1.94 Å / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2895 / CC1/2: 0.884

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→39.07 Å / SU ML: 0.2451 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9651
RfactorNum. reflection% reflection
Rfree0.2328 2381 5.23 %
Rwork0.1848 --
obs0.1874 45498 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3789 0 54 402 4245
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053950
X-RAY DIFFRACTIONf_angle_d0.75835345
X-RAY DIFFRACTIONf_chiral_restr0.0524627
X-RAY DIFFRACTIONf_plane_restr0.0048660
X-RAY DIFFRACTIONf_dihedral_angle_d12.5751522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.47741250.40812519X-RAY DIFFRACTION99.62
1.94-1.980.28781130.26592535X-RAY DIFFRACTION100
1.98-2.030.29361100.21772589X-RAY DIFFRACTION100
2.03-2.080.32531270.2672521X-RAY DIFFRACTION99.96
2.08-2.130.28441320.22382537X-RAY DIFFRACTION99.85
2.13-2.20.25071470.20352490X-RAY DIFFRACTION100
2.2-2.270.30641270.2252554X-RAY DIFFRACTION99.89
2.27-2.350.23141740.19772501X-RAY DIFFRACTION99.96
2.35-2.440.23761310.18892541X-RAY DIFFRACTION100
2.44-2.550.24591500.1822495X-RAY DIFFRACTION100
2.55-2.690.25761810.18852493X-RAY DIFFRACTION100
2.69-2.860.22381400.17752549X-RAY DIFFRACTION100
2.86-3.080.22051650.17922517X-RAY DIFFRACTION100
3.08-3.390.23471390.17132556X-RAY DIFFRACTION100
3.39-3.880.20421480.15272530X-RAY DIFFRACTION99.93
3.88-4.880.17821340.13992575X-RAY DIFFRACTION100
4.88-39.070.18171380.15792615X-RAY DIFFRACTION99.85

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