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- PDB-9b7c: high-resolution ambient temperature structure of lysozyme soaked ... -

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Basic information

Entry
Database: PDB / ID: 9b7c
Titlehigh-resolution ambient temperature structure of lysozyme soaked with sodium iodide
ComponentsLysozyme C
KeywordsHYDROLASE / lysozyme
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
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-like domain superfamily
Similarity search - Domain/homology
IODIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsWang, H.K. / Greisman, J.B. / Hekstra, D.R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DGE 2140743 United States
National Science Foundation (NSF, United States)DGE1745303 United States
National Institutes of Health/Office of the DirectorDP2-GM141000 United States
CitationJournal: To Be Published
Title: Bayesian Priors for Comparative Crystallography
Authors: Hekstra, D.R. / Wang, H.K.
History
DepositionMar 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2024Provider: 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)14,9197
Polymers14,3311
Non-polymers5886
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.405, 79.405, 37.837
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-202-

GOL

21A-206-

IOD

31A-326-

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 natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.05 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG4000, sodium citrate, 100 mM sodium iodide, glycerol

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.03752 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03752 Å / Relative weight: 1
ReflectionResolution: 1.1→79.41 Å / Num. obs: 85383 / % possible obs: 91.3 % / Redundancy: 123.4 % / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.005 / Rrim(I) all: 0.06 / Χ2: 0.95 / Net I/σ(I): 53.6
Reflection shellResolution: 1.1→1.12 Å / % possible obs: 22.3 % / Redundancy: 18.1 % / Rmerge(I) obs: 2.278 / Num. measured all: 9534 / Num. unique obs: 526 / CC1/2: 0.44 / Rpim(I) all: 0.527 / Rrim(I) all: 2.344 / Χ2: 0.85 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Aimless0.7.4data scaling
DIALS3.2.0data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→56.15 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 10.17 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.1229 4061 4.76 %
Rwork0.1105 --
obs0.1111 85383 91.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.1→56.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 16 84 1101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111227
X-RAY DIFFRACTIONf_angle_d1.0491671
X-RAY DIFFRACTIONf_dihedral_angle_d13.22464
X-RAY DIFFRACTIONf_chiral_restr0.099163
X-RAY DIFFRACTIONf_plane_restr0.012228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1-1.110.3729280.3312508X-RAY DIFFRACTION17
1.11-1.130.3021650.27791161X-RAY DIFFRACTION38
1.13-1.140.2088670.24681739X-RAY DIFFRACTION56
1.14-1.160.25111210.21842128X-RAY DIFFRACTION70
1.16-1.170.17681360.19772527X-RAY DIFFRACTION83
1.17-1.190.19561150.16942740X-RAY DIFFRACTION89
1.19-1.210.14261530.13682947X-RAY DIFFRACTION95
1.21-1.230.1491290.12023013X-RAY DIFFRACTION98
1.23-1.250.1381600.10443029X-RAY DIFFRACTION99
1.25-1.270.12241480.09843086X-RAY DIFFRACTION100
1.27-1.290.09531610.08643074X-RAY DIFFRACTION100
1.29-1.320.11461480.08053069X-RAY DIFFRACTION100
1.32-1.340.1161410.07973074X-RAY DIFFRACTION100
1.34-1.370.10761490.08373115X-RAY DIFFRACTION100
1.37-1.40.10231710.08453041X-RAY DIFFRACTION100
1.4-1.440.1071560.08573084X-RAY DIFFRACTION100
1.44-1.480.0981790.07763044X-RAY DIFFRACTION100
1.48-1.520.08891550.0683097X-RAY DIFFRACTION100
1.52-1.570.08791590.06783060X-RAY DIFFRACTION100
1.57-1.630.09241700.06873047X-RAY DIFFRACTION100
1.63-1.690.07721670.073077X-RAY DIFFRACTION100
1.69-1.770.0951520.0813067X-RAY DIFFRACTION100
1.77-1.860.08611570.08073060X-RAY DIFFRACTION100
1.86-1.980.09611500.08283089X-RAY DIFFRACTION100
1.98-2.130.10761310.08743102X-RAY DIFFRACTION100
2.13-2.340.11371560.10013077X-RAY DIFFRACTION100
2.34-2.680.13081290.11783105X-RAY DIFFRACTION100
2.68-3.380.14141490.13453092X-RAY DIFFRACTION100
3.38-56.150.14731590.14273070X-RAY DIFFRACTION100

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