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- PDB-4owd: Crystal structure of MltF from Pseudomonas aeruginosa complexed w... -

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Basic information

Entry
Database: PDB / ID: 4owd
TitleCrystal structure of MltF from Pseudomonas aeruginosa complexed with cysteine
ComponentsMembrane-bound lytic murein transglycosylase F
KeywordsLYASE / Lytic transglycosylase / glycosyltransferase / ABC substrate binding-like domain / peptidoglycan
Function / homology
Function and homology information


: / lytic transglycosylase activity / peptidoglycan catabolic process / cell wall organization / cell outer membrane / cell wall macromolecule catabolic process
Similarity search - Function
Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Membrane-bound lytic murein transglycosylase F / Prokaryotic transglycosylase, active site / Prokaryotic transglycosylases signature. / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Lysozyme-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / Membrane-bound lytic murein transglycosylase F
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.21 Å
AuthorsReddem, E. / Thunnissen, A.M.W.H.
CitationJournal: To Be Published
Title: Crystal structure of MltF from Pseudomonas aeruginosa complexed with cysteine
Authors: Reddem, E. / Thunnissen, A.M.W.H.
History
DepositionJan 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane-bound lytic murein transglycosylase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4433
Polymers49,2861
Non-polymers1572
Water5,350297
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.601, 82.618, 96.235
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsGel filtration confirms that the protein is a monomer in solution

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Components

#1: Protein Membrane-bound lytic murein transglycosylase F / Murein lyase F


Mass: 49286.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: mltF, PA3764 / Plasmid: pBADnLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: Q9HXN1, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-CYS / CYSTEINE / Cysteine


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.28 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 0.2 M MgCl2, 20% (w/v) PEG8000

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.878→62.686 Å / Num. obs: 95977 / % possible obs: 93.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 20.88 Å2 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.02 / Rrim(I) all: 0.045 / Rsym value: 0.04 / Net I/av σ(I): 15.135 / Net I/σ(I): 22.7 / Num. measured all: 95983
Reflection shellResolution: 2.21→2.32 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.079 / Mean I/σ(I) obs: 11.4 / % possible all: 94.9

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALA3.3.20data scaling
PHASERphasing
REFMAC5refinement
PDB_EXTRACT3.14data extraction
RefinementResolution: 2.21→33.76 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.637 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.231 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 1160 5.2 %RANDOM
Rwork0.1919 21153 --
obs0.1943 22313 92.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.55 Å2 / Biso mean: 21.603 Å2 / Biso min: 6.23 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: final / Resolution: 2.21→33.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3429 0 8 297 3734
Biso mean--26.05 26.7 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193516
X-RAY DIFFRACTIONr_bond_other_d0.0010.023345
X-RAY DIFFRACTIONr_angle_refined_deg0.9091.964754
X-RAY DIFFRACTIONr_angle_other_deg0.67637669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5915429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83723.702181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77515612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2051533
X-RAY DIFFRACTIONr_chiral_restr0.0510.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02845
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 88 -
Rwork0.212 1567 -
all-1655 -
obs--93.71 %

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