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- PDB-4g9s: Crystal structure of Escherichia coli PliG in complex with Atlant... -

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Basic information

Entry
Database: PDB / ID: 4g9s
TitleCrystal structure of Escherichia coli PliG in complex with Atlantic salmon g-type lysozyme
Components
  • Goose-type lysozyme
  • Inhibitor of g-type lysozyme
KeywordsHYDROLASE/HYDROLASE INHIBITOR / hydrolase inhibitor / lysozyme / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


lysozyme inhibitor activity / peptidoglycan catabolic process / defense response / lysozyme / lysozyme activity / outer membrane-bounded periplasmic space / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Glycoside hydrolase, family 23 / Jelly Rolls - #380 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Jelly Rolls ...Glycoside hydrolase, family 23 / Jelly Rolls - #380 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Transglycosylase SLT domain 1 / Transglycosylase SLT domain / Lysozyme - #10 / Lysozyme / Lysozyme-like domain superfamily / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CITRATE ANION / Lysozyme g / Inhibitor of g-type lysozyme
Similarity search - Component
Biological speciesSalmo salar (Atlantic salmon)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsLeysen, S. / Vanderkelen, L. / Weeks, S.D. / Michiels, C.W. / Strelkov, S.V.
CitationJournal: Cell.Mol.Life Sci. / Year: 2013
Title: Structural basis of bacterial defense against g-type lysozyme-based innate immunity.
Authors: Leysen, S. / Vanderkelen, L. / Weeks, S.D. / Michiels, C.W. / Strelkov, S.V.
History
DepositionJul 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Sep 13, 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_initial_refinement_model / 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 / _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: Goose-type lysozyme
B: Inhibitor of g-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8584
Polymers33,6342
Non-polymers2252
Water9,746541
1
A: Goose-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1302
Polymers21,0951
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inhibitor of g-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7282
Polymers12,5391
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.182, 132.182, 42.902
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Goose-type lysozyme / Lysozyme g


Mass: 21094.729 Da / Num. of mol.: 1 / Fragment: UNP residues 22-200 / Mutation: A133V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmo salar (Atlantic salmon) / Gene: lysG, LYG / Plasmid: pQE2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6PZ97
#2: Protein Inhibitor of g-type lysozyme


Mass: 12538.815 Da / Num. of mol.: 1 / Fragment: UNP residues 23-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pliG, ycgK / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76002
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.8M tri-ammonium citrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSOLEIL PROXIMA 110.8, 1.8233
SOLEIL PROXIMA 12
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystalSINGLE WAVELENGTHMx-ray1
2Kirkpatrick-Baez pair of bi-morph mirrors plus channel cut cryogenically cooled monochromator crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.81
21.82331
ReflectionResolution: 0.95→43.43 Å / Num. obs: 265542 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2
Reflection shellResolution: 0.95→1 Å / Redundancy: 3 % / Mean I/σ(I) obs: 0.7 / Num. unique all: 36278 / % possible all: 92.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MGW AND 4DY3

3mgw

4dy3


Resolution: 0.95→43.267 Å / SU ML: 0.12 / σ(F): 1.33 / Phase error: 15.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1363 2635 1 %RANDOM
Rwork0.1293 ---
all0.1294 263862 --
obs0.1294 263907 98.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.95→43.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 14 541 2928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062623
X-RAY DIFFRACTIONf_angle_d1.1493563
X-RAY DIFFRACTIONf_dihedral_angle_d13.2111031
X-RAY DIFFRACTIONf_chiral_restr0.068366
X-RAY DIFFRACTIONf_plane_restr0.006469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.95-0.96660.39681180.353910942X-RAY DIFFRACTION78
0.9666-0.98520.33191340.33612989X-RAY DIFFRACTION93
0.9852-1.00530.30091490.305213597X-RAY DIFFRACTION98
1.0053-1.02720.33891480.277613742X-RAY DIFFRACTION98
1.0272-1.05110.26791680.246913778X-RAY DIFFRACTION99
1.0511-1.07740.2331470.206213856X-RAY DIFFRACTION99
1.0774-1.10650.1791420.171913821X-RAY DIFFRACTION99
1.1065-1.13910.14841470.14713939X-RAY DIFFRACTION99
1.1391-1.17590.12671500.130113905X-RAY DIFFRACTION100
1.1759-1.21790.12781350.124113898X-RAY DIFFRACTION100
1.2179-1.26670.11861510.114413971X-RAY DIFFRACTION100
1.2667-1.32430.12521550.103913990X-RAY DIFFRACTION100
1.3243-1.39410.10721320.095314011X-RAY DIFFRACTION100
1.3941-1.48150.09741170.088814057X-RAY DIFFRACTION100
1.4815-1.59590.09421230.085414026X-RAY DIFFRACTION100
1.5959-1.75650.09871400.091114029X-RAY DIFFRACTION100
1.7565-2.01060.09861280.094214100X-RAY DIFFRACTION100
2.0106-2.53320.10821270.108814199X-RAY DIFFRACTION100
2.5332-43.31170.14121240.143214377X-RAY DIFFRACTION100

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