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- PDB-5dl9: Structure of Tetragonal Lysozyme in complex with Iodine solved by... -

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Basic information

Entry
Database: PDB / ID: 5dl9
TitleStructure of Tetragonal Lysozyme in complex with Iodine solved by UWO Students
ComponentsLysozyme C
KeywordsHYDROLASE / Glycoside Hydrolase / Enzyme
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / IODIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.38 Å
AuthorsBednarski, R. / Cirricione, N. / Greco, A. / Hodgson, R. / Kent, S. / McGowan, J. / Notherm, B. / Patt, M. / Vue, L. / Bianchetti, C.M.
CitationJournal: To Be Published
Title: Structure of Tetragonal Lysozyme in complex with Iodine solved by UWO Students
Authors: Bednarski, R. / Cirricione, N. / Greco, A. / Hodgson, R. / Kent, S. / McGowan, J. / Notherm, B. / Patt, M. / Vue, L. / Bianchetti, C.M.
History
DepositionSep 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,45615
Polymers14,3311
Non-polymers1,12514
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.459, 79.459, 37.042
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-352-

HOH

21A-398-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Escherichia coli (E. coli) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.04 Å3/Da / Density % sol: 39.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: Protein Solution (60 mg/ml protein in 0.1M Na acetate pH 4.6) mixed in a 1:1 ratio with the Well Solution (10% NaCl buffered in 0.1 M Na acetate pH 4.5). Cryoprotected in 10% NaI, 0.1 M Na ...Details: Protein Solution (60 mg/ml protein in 0.1M Na acetate pH 4.6) mixed in a 1:1 ratio with the Well Solution (10% NaCl buffered in 0.1 M Na acetate pH 4.5). Cryoprotected in 10% NaI, 0.1 M Na acetate pH 4.5 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.23→50 Å / Num. obs: 31941 / % possible obs: 92 % / Redundancy: 12.5 % / Biso Wilson estimate: 11.79 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.02 / Rrim(I) all: 0.076 / Χ2: 2.388 / Net I/av σ(I): 51.357 / Net I/σ(I): 12.4 / Num. measured all: 400124
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.23-1.254.20.7138650.7870.3480.7990.64551.6
1.25-1.275.70.70110120.8020.3020.7680.66758.8
1.27-1.37.20.62211530.8890.2350.6680.73568.2
1.3-1.328.40.56813100.910.20.6060.68576.2
1.32-1.359.10.50914480.9280.1720.540.72485.3
1.35-1.3910.40.41216470.9570.130.4330.78896.5
1.39-1.4211.50.34617160.9720.1050.3630.915100
1.42-1.4613.10.28517120.9790.0810.2971.027100
1.46-1.514.20.25316990.9860.0690.2631.142100
1.5-1.5514.20.21317270.990.0580.2211.305100
1.55-1.6114.30.17717250.9940.0480.1831.514100
1.61-1.6714.30.1517160.9940.0410.1561.8499.9
1.67-1.7514.30.13717430.9950.0370.1422.096100
1.75-1.8414.30.11517310.9960.0310.122.37899.9
1.84-1.9514.30.09717300.9970.0260.12.93100
1.95-2.114.30.08717470.9980.0240.0913.73100
2.1-2.3114.30.08617670.9970.0230.0894.745100
2.31-2.6514.30.08217750.9960.0220.0855.273100
2.65-3.3414.10.05917980.9990.0160.0614.353100
3.34-5013.20.04119200.9990.0120.0433.22199.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.38→33.573 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 15.23 / Stereochemistry target values: MLHL
Details: The data was collected to 1.23A, but the model was refined against data to 1.38A
RfactorNum. reflection% reflection
Rfree0.1843 1561 6.27 %
Rwork0.1545 23322 -
obs0.1564 24883 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.76 Å2 / Biso mean: 15.2893 Å2 / Biso min: 5.92 Å2
Refinement stepCycle: final / Resolution: 1.38→33.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 44 98 1143
Biso mean--18.67 25.18 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121081
X-RAY DIFFRACTIONf_angle_d1.3221441
X-RAY DIFFRACTIONf_chiral_restr0.065148
X-RAY DIFFRACTIONf_plane_restr0.007188
X-RAY DIFFRACTIONf_dihedral_angle_d12.317391
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.42460.16551370.12772056219398
1.4246-1.47550.17551390.12032060219999
1.4755-1.53460.15321400.1132084222499
1.5346-1.60440.18311400.113320872227100
1.6044-1.6890.16111400.118721082248100
1.689-1.79480.14181390.125220892228100
1.7948-1.93340.17341420.12421072249100
1.9334-2.12790.1421420.133421252267100
2.1279-2.43570.15731440.142521472291100
2.4357-3.06850.19881450.167521652310100
3.0685-33.5830.22921530.199922942447100

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