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- PDB-4p11: Native crystal structure of MltF Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4p11
TitleNative crystal structure of MltF Pseudomonas aeruginosa
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
Membrane-bound lytic murein transglycosylase F
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.891 Å
AuthorsReddem, E. / Thunnissen, A.M.W.H.
CitationJournal: To Be Published
Title: Native crystal structure of MltF Pseudomonas aeruginosa
Authors: Reddem, E. / Thunnissen, A.M.W.H.
History
DepositionFeb 24, 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
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
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
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)49,3714
Polymers49,2861
Non-polymers843
Water8,845491
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.258, 82.473, 96.921
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsBased on SAXS, Gel filtration and DLS, protein is 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 / Details (production host): 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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#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.: 491 / 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: 2.49 Å3/Da / Density % sol: 50.05 %
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: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.873
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.8→48.46 Å / Num. obs: 43654 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 18.08 Å2 / Rpim(I) all: 0.044 / Rrim(I) all: 0.103 / Rsym value: 0.092 / Net I/av σ(I): 7.043 / Net I/σ(I): 12 / Num. measured all: 209480
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.1 % / % possible all: 99.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.15data scaling
SHARPphasing
WARPmodel building
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.891→41.781 Å / FOM work R set: 0.9002 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1852 1871 5.02 %
Rwork0.1506 35404 -
obs0.1524 37275 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.02 Å2 / Biso mean: 24.08 Å2 / Biso min: 7.28 Å2
Refinement stepCycle: final / Resolution: 1.891→41.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 3 491 3919
Biso mean--29.48 31.11 -
Num. residues----428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053523
X-RAY DIFFRACTIONf_angle_d0.8514753
X-RAY DIFFRACTIONf_chiral_restr0.032504
X-RAY DIFFRACTIONf_plane_restr0.004628
X-RAY DIFFRACTIONf_dihedral_angle_d13.9721328
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8906-1.94170.22721310.18592296242783
1.9417-1.99880.21071290.17732703283299
1.9988-2.06330.24261390.1642735287499
2.0633-2.13710.21151320.153127282860100
2.1371-2.22260.19121490.142527452894100
2.2226-2.32380.1621430.146427392882100
2.3238-2.44630.19811510.14852737288899
2.4463-2.59950.18561540.14662739289399
2.5995-2.80020.17471480.15842759290799
2.8002-3.08190.23751500.16042753290399
3.0819-3.52770.17041440.15182768291299
3.5277-4.44370.15051550.12582798295399
4.4437-41.79170.17161460.15492904305097
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1489-0.0308-0.46131.77140.57791.88750.020.06790.0963-0.13560.0434-0.2418-0.11340.1631-0.03790.08470.00130.01370.09610.00840.127829.8932-2.1408-27.0846
23.95250.81780.04961.30.26961.0317-0.00310.1044-0.1965-0.02870.0036-0.02150.0824-0.1027-0.00080.1168-0.0096-0.00060.1146-0.00780.06171.1884-20.4596-22.2559
31.30110.0961-0.45251.2375-0.90672.34210.0301-0.2334-0.03760.2077-0.08070.0347-0.03750.13990.06670.1111-0.01720.00510.1407-0.0160.08081.7127-18.2351-4.1089
41.34380.3508-0.00823.47490.27141.01960.0757-0.16120.15920.2263-0.06680.06270.013-0.02330.00180.082-0.00060.00580.1233-0.00850.097418.978910.0475-8.9209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 125 through 229 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 273 through 351 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 352 through 459 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 32 through 124 ) or chain 'A' and (resid 230 through 272 )A0

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