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- PDB-8yq7: Acinetobacter baumannii membrane-bound lytic murein transglycosylase G -

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Basic information

Entry
Database: PDB / ID: 8yq7
TitleAcinetobacter baumannii membrane-bound lytic murein transglycosylase G
ComponentsEndolytic murein transglycosylase
KeywordsLYASE / Acinetobacter baumannii / membrane-bound lytic murein transglycosylase G / MltG / HYDROLASE
Function / homologypeptidoglycan lytic transglycosylase / Endolytic murein transglycosylase / YceG-like family / lytic endotransglycosylase activity / peptidoglycan biosynthetic process / cell wall organization / plasma membrane / Endolytic murein transglycosylase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsJang, H.S. / Park, H.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Acinetobacter baumannii membrane-bound lytic murein transglycosylase G
Authors: Jang, H.S. / Park, H.H.
History
DepositionMar 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolytic murein transglycosylase
B: Endolytic murein transglycosylase
C: Endolytic murein transglycosylase
D: Endolytic murein transglycosylase
E: Endolytic murein transglycosylase
F: Endolytic murein transglycosylase


Theoretical massNumber of molelcules
Total (without water)182,0326
Polymers182,0326
Non-polymers00
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.860, 162.370, 79.110
Angle α, β, γ (deg.)90.000, 108.957, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Endolytic murein transglycosylase / Peptidoglycan polymerization terminase


Mass: 30338.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: mltG, ABUW_1023, EA686_04105, F2P40_13190, HBK86_13510
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D5YEP5, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 17%(w/v) PEG 10000, 0.1M BisTris pH 5.5, 0.1M Ammonium Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97959 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 2.67→29.47 Å / Num. obs: 47837 / % possible obs: 99.61 % / Redundancy: 7.1 % / Biso Wilson estimate: 58.28 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.28
Reflection shellResolution: 2.67→2.765 Å / Num. unique obs: 4749 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACTdata extraction
HKL-2000data collection
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→29.47 Å / SU ML: 0.4429 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.3487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2729 2389 5 %
Rwork0.2385 45382 -
obs0.2402 47771 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.39 Å2
Refinement stepCycle: LAST / Resolution: 2.67→29.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10299 0 0 58 10357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006910514
X-RAY DIFFRACTIONf_angle_d0.96114372
X-RAY DIFFRACTIONf_chiral_restr0.05181685
X-RAY DIFFRACTIONf_plane_restr0.00721883
X-RAY DIFFRACTIONf_dihedral_angle_d19.33373682
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.720.39361410.35072685X-RAY DIFFRACTION99.51
2.72-2.780.37151390.33052621X-RAY DIFFRACTION99.39
2.78-2.850.37791400.3232670X-RAY DIFFRACTION99.4
2.85-2.920.37411410.32562661X-RAY DIFFRACTION99.64
2.92-30.36161390.30282644X-RAY DIFFRACTION99.82
3-3.090.3431410.2882669X-RAY DIFFRACTION99.72
3.09-3.190.33151400.28492650X-RAY DIFFRACTION99.54
3.19-3.30.33131400.26942678X-RAY DIFFRACTION99.79
3.3-3.430.33921400.26632656X-RAY DIFFRACTION99.82
3.43-3.590.25871410.2442680X-RAY DIFFRACTION99.75
3.59-3.780.24741410.21852683X-RAY DIFFRACTION99.89
3.78-4.010.2851390.21942662X-RAY DIFFRACTION99.89
4.01-4.320.24141400.20492665X-RAY DIFFRACTION100
4.32-4.750.23871410.1952691X-RAY DIFFRACTION100
4.75-5.440.23771420.22212691X-RAY DIFFRACTION99.93
5.44-6.840.23421410.23452682X-RAY DIFFRACTION99.79
6.84-29.470.22231430.20512694X-RAY DIFFRACTION98.82

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