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- PDB-8ezu: Lysozyme Anomalous Dataset at 273 K and 7.1 keV -

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Basic information

Entry
Database: PDB / ID: 8ezu
TitleLysozyme Anomalous Dataset at 273 K and 7.1 keV
ComponentsLysozyme C
KeywordsHYDROLASE
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: 1.901 Å
AuthorsDoukov, T. / Yabukarski, F. / Herschlag, D.
Funding support United States, France, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1714723 United States
Human Frontier Science Program (HFSP) France
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Obtaining anomalous and ensemble information from protein crystals from 220 K up to physiological temperatures.
Authors: Doukov, T. / Herschlag, D. / Yabukarski, F.
History
DepositionNov 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,82915
Polymers14,3311
Non-polymers49814
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.322, 77.322, 37.082
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-342-

HOH

21A-364-

HOH

31A-374-

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: Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: 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: 1.93 Å3/Da / Density % sol: 36.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 5 uL of 0.6 M Sodium Chloride in 100 mM Sodium Acetate buffer pH 4.5 and 25% ethylene glycol were mixed with 5 uL 100 mg/mL lysozyme in 100 mM Sodium Acetate.

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Data collection

DiffractionMean temperature: 273 K / Ambient temp details: Oxford Cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.7462 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 19, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7462 Å / Relative weight: 1
ReflectionResolution: 1.9→38.663 Å / Num. obs: 9255 / % possible obs: 99.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 26.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.028 / Net I/σ(I): 29.7
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 9.1 / Num. unique obs: 573 / CC1/2: 0.988 / Rpim(I) all: 0.082 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→38.663 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.136 / SU B: 5.145 / SU ML: 0.077 / Average fsc free: 0.9796 / Average fsc work: 0.9892 / Cross valid method: FREE R-VALUE / ESU R: 0.136 / ESU R Free: 0.12
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1705 478 5.179 %
Rwork0.1334 8752 -
all0.135 --
obs-9230 99.258 %
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: 22.132 Å2
Baniso -1Baniso -2Baniso -3
1--0.388 Å20 Å20 Å2
2---0.388 Å20 Å2
3---0.775 Å2
Refinement stepCycle: LAST / Resolution: 1.901→38.663 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 17 79 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0111084
X-RAY DIFFRACTIONr_bond_other_d0.0010.016946
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.6391475
X-RAY DIFFRACTIONr_angle_other_deg0.5521.5632210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7575143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.966515
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82310183
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.9691057
X-RAY DIFFRACTIONr_chiral_restr0.0810.2153
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02244
X-RAY DIFFRACTIONr_nbd_refined0.2390.2238
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2030.2834
X-RAY DIFFRACTIONr_nbtor_refined0.1790.2524
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.2536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3750.260
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2050.212
X-RAY DIFFRACTIONr_nbd_other0.1860.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.215
X-RAY DIFFRACTIONr_mcbond_it2.3142.772531
X-RAY DIFFRACTIONr_mcbond_other2.3152.769531
X-RAY DIFFRACTIONr_mcangle_it2.895.171666
X-RAY DIFFRACTIONr_mcangle_other2.8975.179667
X-RAY DIFFRACTIONr_scbond_it4.4553.582553
X-RAY DIFFRACTIONr_scbond_other4.4523.592554
X-RAY DIFFRACTIONr_scangle_it6.4046.329801
X-RAY DIFFRACTIONr_scangle_other6.46.338802
X-RAY DIFFRACTIONr_lrange_it7.46522.4941328
X-RAY DIFFRACTIONr_lrange_other7.41721.541315
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.901-1.950.256330.1546330.1596810.9670.98897.79740.141
1.95-2.0040.211270.1396020.1426290.9810.9881000.125
2.004-2.0610.196330.1276150.136480.9770.9891000.115
2.061-2.1250.163400.1235560.1265960.9830.9911000.114
2.125-2.1940.178410.1165740.1216150.9820.9911000.111
2.194-2.2710.147280.1235460.1245800.9860.99198.96550.117
2.271-2.3560.22340.1285270.1335610.9670.991000.123
2.356-2.4520.233310.1265180.1315490.9780.9891000.121
2.452-2.5610.22180.1374960.145140.9630.9881000.132
2.561-2.6850.222150.1334930.1355080.9670.9881000.13
2.685-2.830.125270.1384430.1374700.9890.9881000.136
2.83-30.147230.1384300.1394540.9840.98999.77970.139
3-3.2060.23150.1324150.1364320.9840.98999.5370.136
3.206-3.4610.14190.1263860.1274070.9870.9999.50860.134
3.461-3.7880.152250.1163400.1183680.9870.99399.18480.127
3.788-4.230.115170.1173270.1173470.9910.99399.13540.13
4.23-4.8750.139200.1212820.1223070.9890.99298.37130.139
4.875-5.9470.281110.1642480.1692700.9760.98795.92590.183
5.947-8.3130.181150.1831920.1832140.970.98296.7290.201
8.313-38.6630.11360.1841290.181430.990.9794.40560.204
Refinement TLS params.Method: refined / Origin x: 18.992 Å / Origin y: 40.289 Å / Origin z: -0.46 Å
111213212223313233
T0.0026 Å20.0011 Å20.0032 Å2-0.0028 Å20.0019 Å2--0.0196 Å2
L2.5929 °2-1.5101 °2-0.1512 °2-2.8581 °20.1732 °2--1.4191 °2
S0.051 Å °0.0385 Å °0.2095 Å °-0.0654 Å °-0.0515 Å °-0.0513 Å °0.0245 Å °0.0244 Å °0.0005 Å °
Refinement TLS groupSelection: ALL

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