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- PDB-4dzg: Crystal structure of Aeromonas hydrophila PliG, a periplasmic lys... -

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Basic information

Entry
Database: PDB / ID: 4dzg
TitleCrystal structure of Aeromonas hydrophila PliG, a periplasmic lysozyme inhibitor of g-type lysozyme
ComponentsPliG
KeywordsHYDROLASE INHIBITOR / lysozyme inhibitor / g-type lysozyme binding
Function / homologyJelly Rolls - #380 / Jelly Rolls / Sandwich / Mainly Beta / G-type lysozyme inhibitor
Function and homology information
Biological speciesAeromonas hydrophila subsp. hydrophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsLeysen, S. / Theuwis, V. / 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
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: PliG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1862
Polymers12,1511
Non-polymers351
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.259, 76.259, 62.443
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PliG


Mass: 12150.683 Da / Num. of mol.: 1 / Fragment: UNP residues 22-134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila subsp. hydrophila (bacteria)
Strain: ATCC 7966 / NCIB 9240 / Gene: AHA_0125 / Plasmid: pETHSUL / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0KEJ7
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate pH6.5, 1M sodium citrate, 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 26, 2011
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.02→19.06 Å / Num. all: 13867 / Num. obs: 13867 / % possible obs: 98.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 2 / Redundancy: 8.9 % / Rsym value: 0.078 / Net I/σ(I): 16.6
Reflection shellResolution: 2.02→2.13 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 1862 / Rsym value: 0.0678 / % possible all: 92.3

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Processing

Software
NameVersionClassification
XDSdata scaling
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→18.317 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 19.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2072 692 5 %random
Rwork0.1842 ---
obs0.1854 13867 97.76 %-
all-13867 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.64 Å2 / ksol: 0.333 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.3835 Å2-0 Å2-0 Å2
2--2.3835 Å2-0 Å2
3----4.767 Å2
Refinement stepCycle: LAST / Resolution: 2.02→18.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms857 0 1 126 984
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008964
X-RAY DIFFRACTIONf_angle_d1.0731323
X-RAY DIFFRACTIONf_dihedral_angle_d15.582367
X-RAY DIFFRACTIONf_chiral_restr0.077140
X-RAY DIFFRACTIONf_plane_restr0.004177
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0168-2.17230.24891600.252422X-RAY DIFFRACTION93
2.1723-2.39050.26161290.21512609X-RAY DIFFRACTION98
2.3905-2.73540.22151310.20052640X-RAY DIFFRACTION99
2.7354-3.44260.2131370.17522682X-RAY DIFFRACTION100
3.4426-18.31760.17711350.16572785X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 28.573 Å / Origin y: -17.106 Å / Origin z: 18.7633 Å
111213212223313233
T0.1946 Å2-0.0386 Å20.0022 Å2-0.1568 Å20.0067 Å2--0.1592 Å2
L3.1512 °20.5512 °20.3494 °2-2.3695 °2-0.0175 °2--1.9543 °2
S0.0252 Å °-0.019 Å °0.3615 Å °-0.0403 Å °-0.09 Å °0.0036 Å °-0.349 Å °-0.0059 Å °0.0307 Å °
Refinement TLS groupSelection details: all

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