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- PDB-8dyz: Hen lysozyme in tetragonal space group at ambient temperature - d... -

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Basic information

Entry
Database: PDB / ID: 8dyz
TitleHen lysozyme in tetragonal space group at ambient temperature - diffuse scattering dataset
ComponentsLysozyme C
KeywordsHYDROLASE / ROOM TEMPERATURE / DIFFUSE SCATTERING / 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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.272 Å
AuthorsMeisburger, S.P. / Ando, N.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117757 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100008 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124847 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103485 United States
Citation
Journal: Nat Commun / Year: 2023
Title: Robust total X-ray scattering workflow to study correlated motion of proteins in crystals.
Authors: Meisburger, S.P. / Case, D.A. / Ando, N.
#1: Journal: Biorxiv / Year: 2022
Title: Robust total X-ray scattering workflow to study correlated motion of proteins in crystals
Authors: Meisburger, S.P. / Case, D.A. / Ando, N.
History
DepositionAug 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: Database references / Category: citation / citation_author
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,4615
Polymers14,3311
Non-polymers1294
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.632, 79.632, 38.296
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-321-

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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Reservoir contained 1.1 M NaCl, 0.1 M NaOAc pH 4.8. Drops contained 2 microliters each of 40 mg/mL protein and well solution.

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2017 / Details: 100 micron collimator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 1.27→39.82 Å / Num. obs: 32284 / % possible obs: 98 % / Redundancy: 23.8 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.009 / Rrim(I) all: 0.047 / Χ2: 1.06 / Net I/av σ(I): 39.2 / Net I/σ(I): 39.2
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1229 / CC1/2: 0.878 / Rpim(I) all: 0.184 / Rrim(I) all: 0.426 / Χ2: 0.99 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
Coot0.9.5model building
XDS20200131data reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 193L

193l


Resolution: 1.272→39.82 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.981 / SU B: 0.831 / SU ML: 0.016 / Cross valid method: FREE R-VALUE / ESU R: 0.035 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1332 1659 5.15 %
Rwork0.1149 30556 -
all0.116 --
obs-32215 97.885 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.565 Å2
Baniso -1Baniso -2Baniso -3
1-0.198 Å2-0 Å2-0 Å2
2--0.198 Å20 Å2
3----0.396 Å2
Refinement stepCycle: LAST / Resolution: 1.272→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 4 79 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0131057
X-RAY DIFFRACTIONr_bond_other_d0.0040.018981
X-RAY DIFFRACTIONr_angle_refined_deg2.0541.6351436
X-RAY DIFFRACTIONr_angle_other_deg1.5991.5962243
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27720.95263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1415179
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.6651511
X-RAY DIFFRACTIONr_chiral_restr0.1310.2136
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021242
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02288
X-RAY DIFFRACTIONr_nbd_refined0.230.2200
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.2775
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2516
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2457
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.221
X-RAY DIFFRACTIONr_metal_ion_refined0.0580.22
X-RAY DIFFRACTIONr_nbd_other0.1590.215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0330.25
X-RAY DIFFRACTIONr_mcbond_it16.2272.002524
X-RAY DIFFRACTIONr_mcbond_other16.1811.996523
X-RAY DIFFRACTIONr_mcangle_it11.0162.997656
X-RAY DIFFRACTIONr_mcangle_other11.0173.017657
X-RAY DIFFRACTIONr_scbond_it29.2622.925533
X-RAY DIFFRACTIONr_scbond_other29.2352.929534
X-RAY DIFFRACTIONr_scangle_it21.9244.043778
X-RAY DIFFRACTIONr_scangle_other21.9114.047779
X-RAY DIFFRACTIONr_lrange_it18.10924.061204
X-RAY DIFFRACTIONr_lrange_other18.14924.0281200
X-RAY DIFFRACTIONr_rigid_bond_restr30.47232038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.272-1.3050.1691100.171812X-RAY DIFFRACTION80.587
1.305-1.3410.1671160.1222062X-RAY DIFFRACTION93.4764
1.341-1.380.141140.0992089X-RAY DIFFRACTION96.9204
1.38-1.4220.131120.082104X-RAY DIFFRACTION99.9549
1.422-1.4690.1171110.0712023X-RAY DIFFRACTION99.9532
1.469-1.520.1031070.0671956X-RAY DIFFRACTION100
1.52-1.5780.1081150.0691887X-RAY DIFFRACTION99.9501
1.578-1.6420.0831030.061838X-RAY DIFFRACTION99.8971
1.642-1.7150.089910.0691743X-RAY DIFFRACTION99.9455
1.715-1.7990.122790.0791707X-RAY DIFFRACTION100
1.799-1.8960.133850.0831623X-RAY DIFFRACTION100
1.896-2.0110.118780.0831541X-RAY DIFFRACTION100
2.011-2.150.106800.0931428X-RAY DIFFRACTION100
2.15-2.3220.14780.0951335X-RAY DIFFRACTION100
2.322-2.5430.15670.1141257X-RAY DIFFRACTION100
2.543-2.8430.17570.141143X-RAY DIFFRACTION100
2.843-3.2820.144550.1411015X-RAY DIFFRACTION100
3.282-4.0180.117430.124876X-RAY DIFFRACTION100
4.018-5.6750.123310.138702X-RAY DIFFRACTION100
5.675-39.820.19270.224415X-RAY DIFFRACTION99.7743

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