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- PDB-6w7p: Crystal Structure Analysis of Space-grown Lysozyme - Ground experiment -

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Basic information

Entry
Database: PDB / ID: 6w7p
TitleCrystal Structure Analysis of Space-grown Lysozyme - Ground experiment
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: 1.6 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 19, 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)14,4966
Polymers14,3311
Non-polymers1655
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.866, 78.866, 37.155
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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.02 Å3/Da / Density % sol: 38.98 %
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: BL14-1 / Wavelength: 1.19499 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2019
Details: Flat bent collimating Rh coated mirror, toroidal focussing mirror
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 1.6→55.767 Å / Num. obs: 15331 / % possible obs: 96.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 20.7 Å2 / Rpim(I) all: 0.028 / Rrim(I) all: 0.054 / Rsym value: 0.045 / Net I/av σ(I): 9.9 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
1.6-1.6930.6190.9688822880.4260.7550.6191.799.6
1.69-1.792.90.41.9621521530.2780.490.42.599.4
1.79-1.913.20.2313.3651420210.1510.2770.2314.499.5
1.91-2.073.30.1295.9615018910.0840.1550.1297.598.5
2.07-2.263.20.0786.6537017020.0520.0950.07811.497.5
2.26-2.533.20.05612.8475915030.0360.0670.05614.993.8
2.53-2.923.50.04315.2471613490.0270.0510.04319.694.2
2.92-3.583.50.03318.4386011030.020.0390.03325.991.2
3.58-5.063.40.02921.128178360.0170.0340.02928.686.5
5.06-39.4333.60.02721.217524850.0160.0320.02730.182.8

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Phasing

PhasingMethod: molecular replacement

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Processing

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

5kxk


Resolution: 1.6→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.084 / SU ML: 0.071 / SU R Cruickshank DPI: 0.0963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 782 5.1 %RANDOM
Rwork0.17 ---
obs0.1727 14505 95.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.37 Å2 / Biso mean: 28.344 Å2 / Biso min: 16.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.92 Å2
Refinement stepCycle: final / Resolution: 1.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 5 140 1146
Biso mean--30.12 38.93 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191040
X-RAY DIFFRACTIONr_bond_other_d0.0020.02955
X-RAY DIFFRACTIONr_angle_refined_deg1.9431.9041412
X-RAY DIFFRACTIONr_angle_other_deg1.18532176
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.38322.88552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84115170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.3031512
X-RAY DIFFRACTIONr_chiral_restr0.1360.2146
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021229
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02277
LS refinement shellResolution: 1.6→1.641 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 71 -
Rwork0.281 1094 -
all-1165 -
obs--99.32 %

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