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

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Basic information

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


: / peptidoglycan lytic transglycosylase activity / peptidoglycan catabolic process / cell outer membrane / cell wall organization / 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
VALINE / Membrane-bound lytic murein transglycosylase F / :
Similarity search - Component
Biological speciesPseudomonas aeruginosa PADK2_CF510 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsReddem, E. / Thunnissen, A.M.W.H.
CitationJournal: To Be Published
Title: Crystal structure of MltF from Pseudomonas aeruginosa complexed with valine
Authors: Reddem, E. / Thunnissen, A.M.W.H.
History
DepositionFeb 7, 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 / symmetry
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 / _symmetry.Int_Tables_number
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,4042
Polymers49,2861
Non-polymers1171
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.881, 80.671, 89.219
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 / Murein lyase F


Mass: 49286.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PADK2_CF510 (bacteria)
Gene: CF510_16633,MltF,mltF / Plasmid: pBADnLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: I1AEE4, UniProt: A0A0J9X1Z1*PLUS, Lyases; Carbon-oxygen lyases; Acting on polysaccharides
#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.93 Å3/Da / Density % sol: 36.41 %
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) PEG 8000.

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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 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.2→52.88 Å / Num. obs: 19799 / % possible obs: 99.15 % / Redundancy: 4.1 % / Rsym value: 0.073 / Net I/σ(I): 6.9
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 94.7

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.7.0029refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.903 / SU B: 6.688 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.369 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2441 1016 5.2 %RANDOM
Rwork0.1758 18702 --
obs0.1792 19718 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.63 Å2 / Biso mean: 28.9 Å2 / Biso min: 2.49 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2---0 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 8 216 3617
Biso mean--19.2 30.97 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193487
X-RAY DIFFRACTIONr_bond_other_d0.0010.023325
X-RAY DIFFRACTIONr_angle_refined_deg1.6291.9614718
X-RAY DIFFRACTIONr_angle_other_deg0.81337623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3535426
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.34723.672177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84315605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.41532
X-RAY DIFFRACTIONr_chiral_restr0.0930.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213999
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02835
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 77 -
Rwork0.216 1251 -
all-1328 -
obs--92.35 %

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