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- PDB-6w8e: Crystal Structure Analysis of Space-grown Lysozyme -

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Basic information

Entry
Database: PDB / ID: 6w8e
TitleCrystal Structure Analysis of Space-grown Lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / ANTIMICROBIAL PROTEIN / muramidase
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
Lysozyme C / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å
AuthorsFernandez, D. / Russi, S.
CitationJournal: NPJ Microgravity / Year: 2020
Title: Protein structural changes on a CubeSat under rocket acceleration profile.
Authors: Luna, A. / Meisel, J. / Hsu, K. / Russi, S. / Fernandez, D.
History
DepositionMar 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3672
Polymers14,3311
Non-polymers351
Water1086
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.970, 75.970, 34.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lysozyme /


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: B8YK79, UniProt: P00698*PLUS, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 1.76 Å3/Da / Density % sol: 29.1 %
Crystal growTemperature: 296 K / Method: liquid diffusion / pH: 4.6 / Details: PEG 6000, NaCl, Na Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 9, 2019
Details: Flat Si Rh coated M0, Kirkpatrick-Baez flat bent Si M1 & M2
RadiationMonochromator: Liquid nitrogen-cooled double crystal Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.675→53.719 Å / Num. all: 3147 / Num. obs: 3147 / % possible obs: 99.6 % / Redundancy: 6.1 % / Rpim(I) all: 0.037 / Rrim(I) all: 0.093 / Rsym value: 0.085 / Net I/av σ(I): 5.9 / Net I/σ(I): 11.7 / Num. measured all: 19338
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
2.675-2.826.70.77714340.3190.8430.77799.7
2.82-2.996.20.5051.44210.2180.5520.50599.9
2.99-3.25.60.2692.84030.1210.2960.26999.7
3.2-3.456.70.1754.23760.0710.1890.17599.9
3.45-3.786.30.1066.53420.0450.1150.10699.5
3.78-4.235.60.0769.23130.0340.0840.07699.7
4.23-4.886.70.05712.12870.0230.0620.05799.6
4.88-5.985.90.0668.92420.0290.0720.06698.8
5.98-8.465.80.053102000.0230.0580.053100
8.46-53.7194.90.0511.31290.0230.0550.0598.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0135refinement
XDSdata reduction
SCALA3.3.22data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5kxk

5kxk


Resolution: 2.68→30 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.88 / SU B: 17.062 / SU ML: 0.358 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.458
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3063 169 5.4 %RANDOM
Rwork0.2441 ---
obs0.2479 2952 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 125.37 Å2 / Biso mean: 73.562 Å2 / Biso min: 37.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.63 Å20 Å20 Å2
2---1.63 Å20 Å2
3---3.26 Å2
Refinement stepCycle: final / Resolution: 2.68→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms874 0 1 6 881
Biso mean--65.62 52.96 -
Num. residues----118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02895
X-RAY DIFFRACTIONr_bond_other_d0.0030.02795
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.8981216
X-RAY DIFFRACTIONr_angle_other_deg1.04831806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0185115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.09123.78437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29115130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.252155
X-RAY DIFFRACTIONr_chiral_restr0.080.2132
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021040
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02223
LS refinement shellResolution: 2.68→2.744 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.351 9 -
Rwork0.207 207 -
obs--99.54 %

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