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- PDB-8qzg: 1,3 L,D-transpeptidase from Gluconobacter oxydans -

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Basic information

Entry
Database: PDB / ID: 8qzg
Title1,3 L,D-transpeptidase from Gluconobacter oxydans
ComponentsYkuD domain-containing protein
KeywordsTRANSFERASE / transpeptidase / peptidoglycan / Gluconobacter oxydans / cell wall / antibiotics resistance / lipoprotein
Function / homologyL,D-transpeptidase catalytic domain / L,D-transpeptidase catalytic domain-like / peptidoglycan L,D-transpeptidase activity / peptidoglycan biosynthetic process / transferase activity / YkuD domain-containing protein
Function and homology information
Biological speciesGluconobacter oxydans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
Authorster Beek, J. / Berntsson, R.P.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council2016-03599, R.P.-A.B. Sweden
Knut and Alice Wallenberg Foundation Sweden
Citation
Journal: Nat Commun / Year: 2024
Title: A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria.
Authors: Espaillat, A. / Alvarez, L. / Torrens, G. / Ter Beek, J. / Miguel-Ruano, V. / Irazoki, O. / Gago, F. / Hermoso, J.A. / Berntsson, R.P. / Cava, F.
#1: Journal: Biorxiv / Year: 2023
Title: A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha and Betaproteobacteria
Authors: Espaillat, A. / Alvarez, L. / Torrens, G. / Beek, J.T. / Miguel-Ruano, V. / Irazoki, O. / Gago, F. / Hermoso, J.A. / Berntsson, R.P.A. / Cava, F.
History
DepositionOct 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Database references / Category: citation / citation_author

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: YkuD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1173
Polymers36,0581
Non-polymers582
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-23 kcal/mol
Surface area12410 Å2
Unit cell
Length a, b, c (Å)52.778, 56.688, 93.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein YkuD domain-containing protein


Mass: 36058.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Gene: EDC20_10617 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4R4A0U0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Imidazole MES monohydrate (acid) pH 6.5, 30 mM Magnesium chloride hexahydrate, 30 mM Calcium chloride dihydrate, 20% v/v PEG 500* MME; 10 % w/v PEG 20000 (Morpheus A1 condition)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.73→48.41 Å / Num. obs: 29339 / % possible obs: 98.48 % / Observed criterion σ(I): 1.12 / Redundancy: 5.6 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.1108 / Net I/σ(I): 10.48
Reflection shellResolution: 1.732→1.794 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.12 / Num. unique obs: 2614 / CC1/2: 0.383 / CC star: 0.744 / % possible all: 88.03

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Processing

Software
NameVersionClassification
XDSdata scaling
XDSdata reduction
PHASER1.20rc3_4406phasing
Cootmodel building
REFMAC5refinement
PHENIX1.21rc1_5109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.73→48.41 Å / SU ML: 0.2033 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0945
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2048 1530 5.22 %
Rwork0.1704 27766 -
obs0.1722 29296 98.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.1 Å2
Refinement stepCycle: LAST / Resolution: 1.73→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 2 133 2191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00852115
X-RAY DIFFRACTIONf_angle_d0.77232895
X-RAY DIFFRACTIONf_chiral_restr0.0555319
X-RAY DIFFRACTIONf_plane_restr0.0085383
X-RAY DIFFRACTIONf_dihedral_angle_d16.5807797
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.790.32891190.32292216X-RAY DIFFRACTION87.39
1.79-1.850.30721260.26692459X-RAY DIFFRACTION97.51
1.85-1.930.25221290.2162508X-RAY DIFFRACTION99.4
1.93-2.010.22141470.18162523X-RAY DIFFRACTION99.81
2.01-2.120.21771430.17062522X-RAY DIFFRACTION99.89
2.12-2.250.22451260.15972542X-RAY DIFFRACTION100
2.25-2.430.20191700.15622542X-RAY DIFFRACTION100
2.43-2.670.19181400.16132560X-RAY DIFFRACTION99.96
2.67-3.060.21761340.16772572X-RAY DIFFRACTION99.89
3.06-3.850.21021670.16112580X-RAY DIFFRACTION99.89
3.85-48.410.1641290.15792742X-RAY DIFFRACTION99.41
Refinement TLS params.Method: refined / Origin x: -2.7260309625 Å / Origin y: 0.229446970295 Å / Origin z: -1.25038284205 Å
111213212223313233
T0.138001170161 Å2-0.00628062926351 Å2-0.00139655491503 Å2-0.155056967186 Å20.0106484762959 Å2--0.193821363606 Å2
L0.638559364954 °2-0.187010469648 °20.00100135603104 °2-1.21245769046 °20.326148002203 °2--1.25192434161 °2
S-0.010912070377 Å °0.00846269513386 Å °0.0106511688465 Å °-0.0192134531523 Å °0.0173203273182 Å °-0.0338685197722 Å °0.00605929387459 Å °-0.0105201590638 Å °-0.00759349759997 Å °
Refinement TLS groupSelection details: { A|54-B|1 }

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