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- PDB-5d5c: In meso in situ serial X-ray crystallography structure of lysozym... -

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Basic information

Entry
Database: PDB / ID: 5d5c
TitleIn meso in situ serial X-ray crystallography structure of lysozyme at 100 K
ComponentsLysozyme C
KeywordsHYDROLASE
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
ACETIC ACID / BROMIDE ION / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHuang, C.-Y. / Olieric, V. / Diederichs, K. / Wang, M. / Caffrey, M.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1255 Ireland
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures.
Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)15,37211
Polymers14,3311
Non-polymers1,04110
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1200 Å2
ΔGint-9 kcal/mol
Surface area6700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.090, 79.090, 38.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 107 molecules

#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.84 Å3/Da / Density % sol: 33.21 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.5-1 M NaBr, 50-100 mM CH3COONa, pH 4.5, and 15-30 %(v/v) PEG400
PH range: pH 4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 13594 / % possible obs: 99.7 % / Redundancy: 5.5 % / Net I/σ(I): 6.16
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tmu

3tmu


Resolution: 1.7→39.545 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2219 677 4.98 %
Rwork0.1834 --
obs0.1854 13594 94.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→39.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 21 97 1118
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081058
X-RAY DIFFRACTIONf_angle_d1.0221426
X-RAY DIFFRACTIONf_dihedral_angle_d13.267384
X-RAY DIFFRACTIONf_chiral_restr0.049149
X-RAY DIFFRACTIONf_plane_restr0.004186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6767-1.80620.32211000.29271900X-RAY DIFFRACTION71
1.8062-1.98790.30271410.23582684X-RAY DIFFRACTION100
1.9879-2.27560.25581420.18622710X-RAY DIFFRACTION100
2.2756-2.86680.20461420.18282738X-RAY DIFFRACTION100
2.8668-39.5560.19451520.15982885X-RAY DIFFRACTION99

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