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- PDB-3f6z: Crystal structure of Pseudomonas aeruginosa MliC in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3f6z
TitleCrystal structure of Pseudomonas aeruginosa MliC in complex with hen egg white lysozyme
Components
  • Lysozyme C
  • Putative uncharacterized protein
KeywordsHYDROLASE / beta barrel / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell outer membrane / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell outer membrane / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
C-type lysozyme inhibitor / Membrane-bound lysozyme-inhibitor of c-type lysozyme / C-type lysozyme inhibitor / C-type lysozyme inhibitor superfamily / Lysozyme - #10 / Lipocalin / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 ...C-type lysozyme inhibitor / Membrane-bound lysozyme-inhibitor of c-type lysozyme / C-type lysozyme inhibitor / C-type lysozyme inhibitor superfamily / Lysozyme - #10 / Lipocalin / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lysozyme-like domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Membrane-bound lysozyme inhibitor of C-type lysozyme
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHa, N.C. / Yum, S.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Structural basis for the recognition of lysozyme by MliC, a periplasmic lysozyme inhibitor in Gram-negative bacteria.
Authors: Yum, S. / Kim, M.J. / Xu, Y. / Jin, X.L. / Yoo, H.Y. / Park, J.W. / Gong, J.H. / Choe, K.M. / Lee, B.L. / Ha, N.C.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
B: Putative uncharacterized protein
C: Lysozyme C
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)50,7414
Polymers50,7414
Non-polymers00
Water12,196677
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-22 kcal/mol
Surface area19500 Å2
MethodPISA
2
A: Lysozyme C
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,3702
Polymers25,3702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-2 kcal/mol
Surface area11200 Å2
MethodPISA
3
C: Lysozyme C
D: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,3702
Polymers25,3702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-3 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.970, 90.960, 49.730
Angle α, β, γ (deg.)90.000, 98.170, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: white egg / References: UniProt: P00698, lysozyme
#2: Protein Putative uncharacterized protein / MliC


Mass: 11039.226 Da / Num. of mol.: 2 / Fragment: residues 27-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: MliC, PA0867 / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I574
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / 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: 3.88 Å3/Da / Density % sol: 68.32 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0M sodium citrate dehydrate, 0.1M HEPES (pH 7.5) , VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC / Detector: CCD / Date: Jul 10, 2008 / Details: mirrors
RadiationMonochromator: Double mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30.23 Å / Num. all: 35000 / Num. obs: 34458 / % possible obs: 0.997 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 28.5 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 18.6
Reflection shellResolution: 2.3→2.41 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.208 / Mean I/σ(I) obs: 8.5 / Num. unique all: 5028 / Rsym value: 0.208 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
CNS1.2refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPQ

1gpq


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 0.89 / Data cutoff high absF: 2469126 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2692 10 %RANDOM
Rwork0.238 ---
all0.25 27000 --
obs0.25 26881 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.665 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 108.49 Å2 / Biso mean: 28.816 Å2 / Biso min: 9.37 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å2-2 Å2
2--2.62 Å20 Å2
3----0.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 0 677 4111
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 442 9.9 %
Rwork0.243 4001 -
all-4443 -
obs-4420 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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