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- PDB-6qk4: Lytic transglycosylase, LtgG, of Burkholderia pseudomallei. -

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Basic information

Entry
Database: PDB / ID: 6qk4
TitleLytic transglycosylase, LtgG, of Burkholderia pseudomallei.
ComponentsMembrane-bound lytic murein transglycosylase A
KeywordsLYASE / lytic transglycosylase / peptidoglycan / cell division / bacterial pathogenesis / Burkholderia pseudomallei
Function / homology
Function and homology information


: / peptidoglycan turnover / outer membrane / hydrolase activity, hydrolyzing O-glycosyl compounds / cell wall organization / lyase activity
Similarity search - Function
MltA, 3D domain / Lytic transglycosylase MltA, domain B / Membrane-bound lytic murein transglycosylase A / MltA specific insert domain / MltA specific insert domain / 3D domain / 3D domain / RlpA-like domain superfamily
Similarity search - Domain/homology
Murein hydrolase A / Murein hydrolase A
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsJenkins, C.H. / Wallis, R. / Allcock, N. / Barnes, K.B. / Richards, M.I. / Auty, J.M. / Galyov, E.E. / Harding, S.V. / Mukamolova, G.V.
CitationJournal: Sci Rep / Year: 2019
Title: The lytic transglycosylase, LtgG, controls cell morphology and virulence in Burkholderia pseudomallei.
Authors: Jenkins, C.H. / Wallis, R. / Allcock, N. / Barnes, K.B. / Richards, M.I. / Auty, J.M. / Galyov, E.E. / Harding, S.V. / Mukamolova, G.V.
History
DepositionJan 28, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Membrane-bound lytic murein transglycosylase A


Theoretical massNumber of molelcules
Total (without water)37,6841
Polymers37,6841
Non-polymers00
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.570, 59.570, 168.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Membrane-bound lytic murein transglycosylase A / MltA specific insert domain protein / Murein transglycosylase


Mass: 37684.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: mltA, CXQ84_03095, DP49_5753, ERS013345_03240 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A069B8V2, UniProt: Q63QH7*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Bis-tris propane (pH 7.5), containing 0.2 M potassium sodium tartrate and 14% PEG 8K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.73→56.1 Å / Num. obs: 37097 / % possible obs: 99.98 % / Redundancy: 16.3 % / Rsym value: 0.112 / Net I/σ(I): 16.1
Reflection shellResolution: 1.73→1.78 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G5D, 2GAE

2g5d

2gae


Resolution: 1.73→56.093 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.99
RfactorNum. reflection% reflection
Rfree0.2088 1919 5.17 %
Rwork0.176 --
obs0.1777 37102 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.6 Å2
Refinement stepCycle: LAST / Resolution: 1.73→56.093 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 0 0 237 2771
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0172600
X-RAY DIFFRACTIONf_angle_d1.3643540
X-RAY DIFFRACTIONf_dihedral_angle_d3.9721525
X-RAY DIFFRACTIONf_chiral_restr0.089373
X-RAY DIFFRACTIONf_plane_restr0.01473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.77340.27721520.21182435X-RAY DIFFRACTION100
1.7734-1.82130.24081100.19772493X-RAY DIFFRACTION100
1.8213-1.87490.22641480.19312486X-RAY DIFFRACTION100
1.8749-1.93540.24521240.18622475X-RAY DIFFRACTION100
1.9354-2.00460.20051240.17812468X-RAY DIFFRACTION100
2.0046-2.08490.20731300.17292484X-RAY DIFFRACTION100
2.0849-2.17980.21441510.17632473X-RAY DIFFRACTION100
2.1798-2.29470.22471130.17532547X-RAY DIFFRACTION100
2.2947-2.43850.24931210.18312474X-RAY DIFFRACTION100
2.4385-2.62670.23191530.18612513X-RAY DIFFRACTION100
2.6267-2.89110.20641470.19142505X-RAY DIFFRACTION100
2.8911-3.30940.23011490.18352546X-RAY DIFFRACTION100
3.3094-4.16930.18281250.16422579X-RAY DIFFRACTION100
4.1693-56.12280.18581720.16392705X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 18.1261 Å / Origin y: -17.5627 Å / Origin z: 14.09 Å
111213212223313233
T0.0665 Å20.0561 Å20.0357 Å2-0.4164 Å2-0.0076 Å2--0.2007 Å2
L0.1916 °2-0.1096 °2-0.0039 °2-0.291 °20.0204 °2--0.0348 °2
S0.1009 Å °0.0638 Å °0.0152 Å °-0.1716 Å °-0.1214 Å °-0.0499 Å °-0.0512 Å °0.0515 Å °-0.0244 Å °
Refinement TLS groupSelection details: (chain B and resseq 10:348)

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