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- PDB-4dy3: crystal structure of Escherichia coli PliG, a periplasmic lysozym... -

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Basic information

Entry
Database: PDB / ID: 4dy3
Titlecrystal structure of Escherichia coli PliG, a periplasmic lysozyme inhibitor of g-type lysozyme
ComponentsInhibitor of g-type lysozyme
KeywordsHORMONE INHIBITOR / lysozyme inhibitor / g-type lysozyme binding
Function / homology
Function and homology information


lysozyme inhibitor activity / periplasmic space / cytosol
Similarity search - Function
Jelly Rolls - #380 / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Inhibitor of g-type lysozyme
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLeysen, S. / Vanheuverzwijn, S. / Van Asten, K. / Vanderkelen, L. / Michiels, C.W. / Strelkov, S.V.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Structural characterization of the PliG lysozyme inhibitor family.
Authors: Leysen, S. / Vanderkelen, L. / Van Asten, K. / Vanheuverzwijn, S. / Theuwis, V. / Michiels, C.W. / Strelkov, S.V.
History
DepositionFeb 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Inhibitor of g-type lysozyme
B: Inhibitor of g-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2624
Polymers25,0782
Non-polymers1842
Water6,377354
1
A: Inhibitor of g-type lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6312
Polymers12,5391
Non-polymers921
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)12,6312
Polymers12,5391
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.543, 83.543, 31.163
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Inhibitor of g-type lysozyme


Mass: 12538.815 Da / Num. of mol.: 2 / Fragment: UNP residues 23-133
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pliG, ycgK, b1178, JW1167 / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P76002
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M sodium acetate pH5.0, 0.15M NaCl, 25% w/v PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 8, 2010
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→19.69 Å / Num. all: 24224 / Num. obs: 22521 / % possible obs: 93 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 2712 / Rsym value: 0.437 / % possible all: 91.1

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→19.69 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 19.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2135 995 5.1 %RANDOM
Rwork0.1656 ---
obs0.1679 19529 95.77 %-
all-19529 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.867 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2952 Å20 Å2-0 Å2
2--1.2952 Å2-0 Å2
3----2.5904 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 12 354 2138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061894
X-RAY DIFFRACTIONf_angle_d0.962558
X-RAY DIFFRACTIONf_dihedral_angle_d13.973728
X-RAY DIFFRACTIONf_chiral_restr0.068260
X-RAY DIFFRACTIONf_plane_restr0.004338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.89480.25041520.21232479X-RAY DIFFRACTION91
1.8948-2.01340.23061370.17422515X-RAY DIFFRACTION92
2.0134-2.16870.22411500.15522589X-RAY DIFFRACTION95
2.1687-2.38660.24731300.1632644X-RAY DIFFRACTION96
2.3866-2.73120.22961320.16952715X-RAY DIFFRACTION98
2.7312-3.4380.19231600.15532727X-RAY DIFFRACTION98
3.438-19.69260.18741340.16312849X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19880.00770.03731.81-0.04362.1920.0344-0.06130.01420.08770.04360.07650.0547-0.1085-0.04160.08120.0257-0.00350.070.02210.081320.7503-34.4152-2.1643
20.84880.34450.27261.68620.38341.7650.0408-0.0527-0.05680.10360.0576-0.1401-0.08070.1061-0.06540.08010.0058-0.00680.0645-0.02120.100821.1647-6.6279-0.2525
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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