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- PDB-7ufp: Structure of a pseudomurein peptide ligase type E from Methanothe... -

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Basic information

Entry
Database: PDB / ID: 7ufp
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
URIDINE-5'-DIPHOSPHATE / Mur ligase middle domain protein
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionMar 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Mur ligase middle domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1937
Polymers54,3081
Non-polymers8846
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.763, 44.975, 98.046
Angle α, β, γ (deg.)90.000, 98.190, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Mur ligase middle domain protein


Mass: 54308.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Strain: ATCC 43054 / DSM 2088 / JCM 10308 / V24 S / Gene: Mfer_0762 / Production host: Escherichia coli (E. coli) / References: UniProt: E3GZ29
#2: 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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
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: 2.55 Å3/Da / Density % sol: 51.71 %
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: MX2 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2→48.52 Å / Num. obs: 37078 / % possible obs: 99.7 % / Redundancy: 6.7 % / Biso Wilson estimate: 28.86 Å2 / CC1/2: 0.991 / Net I/σ(I): 14
Reflection shellResolution: 2→2.06 Å / Num. unique obs: 2629 / CC1/2: 0.889 / % possible all: 96.1

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Processing

Software
NameVersionClassification
PHENIX1.20rc4_4425refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7jt8

7jt8


Resolution: 2→41.34 Å / SU ML: 0.2166 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.2881
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2286 1833 4.95 %
Rwork0.1802 35207 -
obs0.1824 37040 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.69 Å2
Refinement stepCycle: LAST / Resolution: 2→41.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3675 0 50 184 3909
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00753796
X-RAY DIFFRACTIONf_angle_d0.78535129
X-RAY DIFFRACTIONf_chiral_restr0.0559605
X-RAY DIFFRACTIONf_plane_restr0.0058628
X-RAY DIFFRACTIONf_dihedral_angle_d5.3173498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.26161330.22592610X-RAY DIFFRACTION96.04
2.06-2.120.29661280.21092678X-RAY DIFFRACTION99.57
2.12-2.190.24721430.19782687X-RAY DIFFRACTION100
2.19-2.270.22711660.19782661X-RAY DIFFRACTION99.61
2.27-2.360.28521390.18842716X-RAY DIFFRACTION100
2.36-2.460.24221470.1852676X-RAY DIFFRACTION100
2.46-2.590.26321460.19022705X-RAY DIFFRACTION100
2.59-2.760.20091480.19182679X-RAY DIFFRACTION99.96
2.76-2.970.24891460.19672711X-RAY DIFFRACTION100
2.97-3.270.25271330.18692737X-RAY DIFFRACTION100
3.27-3.740.24111350.17442758X-RAY DIFFRACTION99.97
3.74-4.710.18541320.15712744X-RAY DIFFRACTION99.93
4.71-41.340.20081370.16662845X-RAY DIFFRACTION99.87

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