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- PDB-6ukc: Crystal structure of a lysozyme from Litopenaeus vannamei -

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Basic information

Entry
Database: PDB / ID: 6ukc
TitleCrystal structure of a lysozyme from Litopenaeus vannamei
ComponentsLysozyme
KeywordsHYDROLASE / Litopenaeus vannamei / lysozyme / Innate immunity
Function / homology
Function and homology information


metabolic process / lysozyme / lysozyme activity
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
Biological speciesPenaeus vannamei (Pacific white shrimp)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHernandez-Santoyo, A. / Rodriguez-Romero, A.
CitationJournal: Fish Shellfish Immunol. / Year: 2020
Title: Crystal structure of a C-type lysozyme from Litopenaeus vanamei exhibiting a high binding constant to its chitotriose inhibitor.
Authors: Vargas-Requena, C.L. / Rodriguez-Romero, A. / Garcia-Ramirez, B. / Sotelo-Mundo, R.R. / Hernandez-Santoyo, A.
History
DepositionOct 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8342
Polymers16,7421
Non-polymers921
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.368, 82.368, 38.665
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Lysozyme /


Mass: 16741.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penaeus vannamei (Pacific white shrimp)
Production host: Escherichia coli (E. coli) / References: UniProt: Q95V66, lysozyme
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: HEPES 0.1M, pH 7.5, 20 (w/v) PEG 10,000%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jul 24, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.25→41.18 Å / Num. obs: 6270 / % possible obs: 86.16 % / Redundancy: 2.8 % / CC1/2: 0.996 / Net I/σ(I): 8.2
Reflection shellResolution: 2.25→2.32 Å / Num. unique obs: 6275 / CC1/2: 0.993

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LSY

1lsy


Resolution: 2.25→35.692 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.762 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.52 / ESU R Free: 0.273
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2463 622 9.92 %
Rwork0.1998 --
all0.204 --
obs-6270 86.162 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.065 Å2
Baniso -1Baniso -2Baniso -3
1--0.268 Å2-0.134 Å20 Å2
2---0.268 Å20 Å2
3---0.871 Å2
Refinement stepCycle: LAST / Resolution: 2.25→35.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 6 66 1156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131115
X-RAY DIFFRACTIONr_bond_other_d0.0010.018980
X-RAY DIFFRACTIONr_ext_dist_refined_d0.1980.0182
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.6461500
X-RAY DIFFRACTIONr_angle_other_deg1.3821.5942268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6815132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04721.38972
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19215194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2381511
X-RAY DIFFRACTIONr_chiral_restr0.0680.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021265
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
X-RAY DIFFRACTIONr_nbd_refined0.2130.2221
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.2935
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2545
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.2490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0680.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0250.25
X-RAY DIFFRACTIONr_nbd_other0.1860.232
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.24
X-RAY DIFFRACTIONr_mcbond_it1.662.314531
X-RAY DIFFRACTIONr_mcbond_other1.6592.31530
X-RAY DIFFRACTIONr_mcangle_it2.6143.461662
X-RAY DIFFRACTIONr_mcangle_other2.6123.465663
X-RAY DIFFRACTIONr_scbond_it1.9952.549584
X-RAY DIFFRACTIONr_scbond_other1.9932.553585
X-RAY DIFFRACTIONr_scangle_it3.163.714838
X-RAY DIFFRACTIONr_scangle_other3.1583.718839
X-RAY DIFFRACTIONr_lrange_it5.6842.4074694
X-RAY DIFFRACTIONr_lrange_other5.65442.394660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3090.392460.286445X-RAY DIFFRACTION89.7623
2.309-2.3720.261460.254418X-RAY DIFFRACTION91.5187
2.372-2.4410.262460.224407X-RAY DIFFRACTION89.881
2.441-2.5160.244460.22417X-RAY DIFFRACTION92.9719
2.516-2.5980.334370.212392X-RAY DIFFRACTION88.4536
2.598-2.6890.248410.207351X-RAY DIFFRACTION86.918
2.689-2.7910.267390.199347X-RAY DIFFRACTION87.7273
2.791-2.9040.281340.214336X-RAY DIFFRACTION87.6777
2.904-3.0330.261390.187325X-RAY DIFFRACTION86.052
3.033-3.1810.208340.185300X-RAY DIFFRACTION88.1266
3.181-3.3530.212320.187298X-RAY DIFFRACTION87.766
3.353-3.5560.202350.188260X-RAY DIFFRACTION81.9444
3.556-3.80.252230.176241X-RAY DIFFRACTION78.806
3.8-4.1040.193240.179216X-RAY DIFFRACTION77.4193
4.104-4.4940.277220.162205X-RAY DIFFRACTION78.8194
4.494-5.0220.176230.164196X-RAY DIFFRACTION83.27
5.794-7.0850.407180.212155X-RAY DIFFRACTION83.9806

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