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

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Basic information

Entry
Database: PDB / ID: 7tzi
TitleStructure of a pseudomurein peptide ligase type E from Methanothermobacter thermautotrophicus
ComponentsMur ligase family protein
KeywordsLIGASE / Pseudomurein / pseudomurein peptide ligase / archaeal cell wall / Methanothermobacter thermautotrophicus / pMurE
Function / homology
Function and homology information


biosynthetic process / ligase activity / 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
Mur ligase family protein
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.911 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 15, 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
A: Mur ligase family protein
B: Mur ligase family protein


Theoretical massNumber of molelcules
Total (without water)97,9352
Polymers97,9352
Non-polymers00
Water55831
1
A: Mur ligase family protein


Theoretical massNumber of molelcules
Total (without water)48,9671
Polymers48,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mur ligase family protein


Theoretical massNumber of molelcules
Total (without water)48,9671
Polymers48,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.266, 127.423, 134.736
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Mur ligase family protein


Mass: 48967.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Gene: HA285_03230 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J4MVA9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 2.91 Å3/Da / Density % sol: 57.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM amino acids mix; 0.1 M buffer system 6, pH 8.5; 50% v/v precipitant mix of 25% w/v PEG4000 and 40% w/v 1,2,6-hexanetriol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.91→47.24 Å / Num. obs: 25647 / % possible obs: 99.5 % / Redundancy: 13.6 % / Biso Wilson estimate: 68.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.1 / Net I/σ(I): 3.92
Reflection shellResolution: 2.91→2.94 Å / Num. unique obs: 3964 / CC1/2: 0.834 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7JT8

7jt8


Resolution: 2.911→46.29 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / SU Rfree Blow DPI: 0.365
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 1257 -RANDOM
Rwork0.2119 ---
obs0.2135 25593 99.5 %-
Displacement parametersBiso mean: 74.98 Å2
Baniso -1Baniso -2Baniso -3
1--10.3928 Å20 Å20 Å2
2--3.9745 Å20 Å2
3---6.4183 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.911→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6825 0 0 31 6856
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0096929HARMONIC2
X-RAY DIFFRACTIONt_angle_deg19404HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2434SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1209HARMONIC5
X-RAY DIFFRACTIONt_it6929HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion950SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact5494SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion17.68
LS refinement shellResolution: 2.911→2.94 Å
RfactorNum. reflection% reflection
Rfree0.4388 24 -
Rwork0.3227 --
obs--81.24 %

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