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- PDB-3od9: Crystal structure of PliI-Ah, periplasmic lysozyme inhibitor of I... -

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Basic information

Entry
Database: PDB / ID: 3od9
TitleCrystal structure of PliI-Ah, periplasmic lysozyme inhibitor of I-type lysozyme from Aeromonas hydrophyla
ComponentsPutative exported protein
KeywordsHYDROLASE INHIBITOR / beta sandwich / C-terminal helix
Function / homology
Function and homology information


Periplasmic lysozyme inhibitor of I-type lysozyme / Periplasmic lysozyme inhibitor, I-type / PliI superfamily / Periplasmic lysozyme inhibitor of I-type lysozyme / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / Putative exported protein
Similarity search - Component
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.411 Å
AuthorsLeysen, S. / Van Herreweghe, J.M. / Callewaert, L. / Heirbaut, M. / Buntinx, P. / Michiels, C.W. / Strelkov, S.V.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Molecular Basis of Bacterial Defense against Host Lysozymes: X-ray Structures of Periplasmic Lysozyme Inhibitors PliI and PliC.
Authors: Leysen, S. / Van Herreweghe, J.M. / Callewaert, L. / Heirbaut, M. / Buntinx, P. / Michiels, C.W. / Strelkov, S.V.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,37915
Polymers44,0713
Non-polymers30812
Water9,620534
1
A: Putative exported protein
B: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,62011
Polymers29,3802
Non-polymers2399
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-33 kcal/mol
Surface area12150 Å2
MethodPISA
2
C: Putative exported protein
hetero molecules

C: Putative exported protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5188
Polymers29,3802
Non-polymers1386
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area2280 Å2
ΔGint-47 kcal/mol
Surface area11720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.021, 60.327, 82.187
Angle α, β, γ (deg.)90.000, 115.650, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-180-

HOH

21A-186-

HOH

31C-395-

HOH

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Components

#1: Protein Putative exported protein


Mass: 14690.225 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Strain: ATCC 7966 / NCIB 9240 / Gene: AHA_1205 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0KHJ5
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 534 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.98
Details: 1.2M sodium phosphate, 0.8M potassium hydrogen phosphate, 0.1M CAPS, 0.2M LiCl, pH 6.98, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.41→47.29 Å / Num. obs: 79434 / % possible obs: 91.2 %

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.411→46.435 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8863 / SU ML: 0.18 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 4014 5.05 %
Rwork0.161 --
obs0.1629 79420 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.977 Å2 / ksol: 0.405 e/Å3
Displacement parametersBiso max: 69.29 Å2 / Biso mean: 29.7248 Å2 / Biso min: 12.58 Å2
Baniso -1Baniso -2Baniso -3
1--6.3507 Å2-0 Å2-1.7134 Å2
2--2.4135 Å2-0 Å2
3----7.3247 Å2
Refinement stepCycle: LAST / Resolution: 1.411→46.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 12 534 3280
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062851
X-RAY DIFFRACTIONf_angle_d1.0753884
X-RAY DIFFRACTIONf_chiral_restr0.065437
X-RAY DIFFRACTIONf_plane_restr0.005526
X-RAY DIFFRACTIONf_dihedral_angle_d17.7671068
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.411-1.4280.267560.25531458151450
1.428-1.44540.3122900.23521563165355
1.4454-1.46370.2829950.21031718181361
1.4637-1.4830.2627980.20431905200367
1.483-1.50330.26761140.19951998211271
1.5033-1.52480.23151230.17662251237479
1.5248-1.54750.1891250.17992505263088
1.5475-1.57170.25251450.15562762290796
1.5717-1.59750.17911300.14652758288898
1.5975-1.6250.18161490.14222796294598
1.625-1.65460.18021490.13832780292998
1.6546-1.68640.17721480.13642803295198
1.6864-1.72080.19851580.13092772293098
1.7208-1.75830.16661420.12892833297598
1.7583-1.79920.17351610.12672763292499
1.7992-1.84420.17871260.1322843296999
1.8442-1.8940.16861770.12612794297199
1.894-1.94980.17061380.12582810294899
1.9498-2.01270.14211260.1312852297899
2.0127-2.08460.16081340.13582867300199
2.0846-2.16810.17961660.13352793295999
2.1681-2.26680.15451660.13462842300899
2.2668-2.38630.16521420.14482856299899
2.3863-2.53580.22321600.163628292989100
2.5358-2.73150.2111700.163328473017100
2.7315-3.00640.19311480.159328673015100
3.0064-3.44130.18671710.146228553026100
3.4413-4.33510.18341490.143728893038100
4.3351-46.45990.22361580.1972797295595

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