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- PDB-9b7f: S_SAD structure of HEWL using lossless default compression -

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Basic information

Entry
Database: PDB / ID: 9b7f
TitleS_SAD structure of HEWL using lossless default compression
ComponentsLysozyme C
KeywordsHYDROLASE / lossy compression / intensity preservation / structural information retention / S_SAD phasing
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsJakoncic, J. / Bernstein, H.J. / Soares, A.S. / Horvat, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
Department of Energy (DOE, United States)KP1607011 United States
CitationJournal: To Be Published
Title: Investigation of fast and efficient lossless compression algorithms for macromolecular crystallography experiments
Authors: Jakoncic, J. / Bernstein, H.J. / Soares, A.S. / Horvat, K.
History
DepositionMar 27, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 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)14,95517
Polymers14,3311
Non-polymers62416
Water2,144119
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.895, 78.895, 36.955
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-378-

HOH

21A-416-

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 / Fragment: lyzozyme / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: LYZ / Production host: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.03 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1000 mM NaCl 100 mM NaAcetate pH 4.6 50 mM Glycerol 50 mM Ethylen Glycol Drop= 1 uL + 1uL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.65 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 15, 2023 / Details: KB mirros
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.65 Å / Relative weight: 1
ReflectionResolution: 1.64→19.73 Å / Num. obs: 13089 / % possible obs: 88.9 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.009 / Rrim(I) all: 0.042 / Net I/σ(I): 60.9
Reflection shellResolution: 1.64→1.67 Å / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 8.5 / Num. unique obs: 268 / CC1/2: 0.988 / Rpim(I) all: 0.06 / Rrim(I) all: 0.078

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→19.73 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 1.626 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.112 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1975 689 5.3 %RANDOM
Rwork0.1592 ---
obs0.1611 12353 89.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.13 Å2 / Biso mean: 12.11 Å2 / Biso min: 5.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 1.65→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 28 120 1149
Biso mean--23.2 20.54 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0121123
X-RAY DIFFRACTIONr_angle_refined_deg1.6561.6461511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.85919.45273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22715190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4151516
X-RAY DIFFRACTIONr_chiral_restr0.1040.2141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02871
X-RAY DIFFRACTIONr_mcbond_it0.8130.977535
X-RAY DIFFRACTIONr_mcangle_it1.2951.46672
X-RAY DIFFRACTIONr_scbond_it1.5311.181588
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 23 -
Rwork0.193 287 -
all-310 -
obs--29.38 %

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