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- PDB-4pj2: Crystal structure of Aeromonas hydrophila PliI in complex with Me... -

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Basic information

Entry
Database: PDB / ID: 4pj2
TitleCrystal structure of Aeromonas hydrophila PliI in complex with Meretrix lusoria lysozyme
Components
  • Lysozyme
  • Putative exported protein
KeywordsHydrolase/Hydrolase inhibitor / Lysozyme / Lysozyme inhibitor / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


chitinase activity / metabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / extracellular region / metal ion binding
Similarity search - Function
Periplasmic lysozyme inhibitor of I-type lysozyme / Periplasmic lysozyme inhibitor, I-type / PliI superfamily / Periplasmic lysozyme inhibitor of I-type lysozyme / Invertebrate-type lysozyme / Destabilase / Invertebrate (I)-type lysozyme domain profile. / Lysozyme - #10 / Lipocalin / Lysozyme ...Periplasmic lysozyme inhibitor of I-type lysozyme / Periplasmic lysozyme inhibitor, I-type / PliI superfamily / Periplasmic lysozyme inhibitor of I-type lysozyme / Invertebrate-type lysozyme / Destabilase / Invertebrate (I)-type lysozyme domain profile. / Lysozyme - #10 / Lipocalin / Lysozyme / Lysozyme-like domain superfamily / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Putative exported protein / Lysozyme
Similarity search - Component
Biological speciesAeromonas hydrophila subsp. hydrophila (bacteria)
Meretrix lusoria (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsLeysen, S. / Van Herreweghe, J.M. / Yoneda, K. / Ogata, M. / Usui, T. / Michiels, C.W. / Araki, T. / Strelkov, S.V.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: The structure of the proteinaceous inhibitor PliI from Aeromonas hydrophila in complex with its target lysozyme.
Authors: Leysen, S. / Van Herreweghe, J.M. / Yoneda, K. / Ogata, M. / Usui, T. / Araki, T. / Michiels, C.W. / Strelkov, S.V.
History
DepositionMay 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 25, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / entity_src_nat / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _entity_src_nat.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative exported protein
B: Putative exported protein
C: Lysozyme
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4068
Polymers56,1744
Non-polymers2334
Water10,899605
1
A: Putative exported protein
D: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2955
Polymers28,0872
Non-polymers2083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-4 kcal/mol
Surface area11440 Å2
MethodPISA
2
B: Putative exported protein
C: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1113
Polymers28,0872
Non-polymers241
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-15 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.933, 77.667, 69.380
Angle α, β, γ (deg.)90.00, 108.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative exported protein / Periplasmic lysozyme inhibitor of i-type lysozyme


Mass: 14690.225 Da / Num. of mol.: 2 / Fragment: UNP residues 20-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila subsp. hydrophila (bacteria)
Strain: ATCC 7966 / NCIB 9240 / Gene: AHA_1205 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: A0KHJ5
#2: Protein Lysozyme / / 1 / 4-beta-N-acetylmuramidase


Mass: 13396.573 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meretrix lusoria (invertebrata) / References: UniProt: P86383, lysozyme
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 605 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M DL-malic acid/MES/Tris-base cocktail buffer at pH 5.0 and 25% w/v PEG 1,500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2012
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.24→47.8 Å / Num. obs: 144102 / % possible obs: 95.7 % / Redundancy: 4.3 % / Net I/σ(I): 10.8

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→47.8 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1678 1457 1.01 %
Rwork0.1483 --
obs0.1485 144031 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.24→47.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 14 605 4311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094017
X-RAY DIFFRACTIONf_angle_d1.2895445
X-RAY DIFFRACTIONf_dihedral_angle_d14.0591545
X-RAY DIFFRACTIONf_chiral_restr0.074574
X-RAY DIFFRACTIONf_plane_restr0.006721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.28380.28841420.26813129X-RAY DIFFRACTION88
1.2838-1.33520.2241400.21913866X-RAY DIFFRACTION93
1.3352-1.39590.20511310.17814016X-RAY DIFFRACTION94
1.3959-1.46950.18351630.157314158X-RAY DIFFRACTION95
1.4695-1.56160.16681330.145514238X-RAY DIFFRACTION96
1.5616-1.68220.18041430.126114388X-RAY DIFFRACTION96
1.6822-1.85150.15411560.121114424X-RAY DIFFRACTION97
1.8515-2.11940.16591460.121314601X-RAY DIFFRACTION98
2.1194-2.67020.15521490.142114741X-RAY DIFFRACTION98
2.6702-47.840.16211540.155815013X-RAY DIFFRACTION99

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