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- PDB-5yin: Hen egg-white lysozyme precipitant-free orthorhombic form -

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Basic information

Entry
Database: PDB / ID: 5yin
TitleHen egg-white lysozyme precipitant-free orthorhombic form
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
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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsSuzuki, Y. / Tsuge, H. / Uehara, Y.
CitationJournal: CRYST.GROWTH DES. / Year: 2018
Title: Precipitant-free lysozyme crystals grown by centrifugal concentration reveal structural changes
Authors: Suzuki, Y. / Tsuge, H. / Hondoh, H. / Kato, Y. / Uehara, Y. / Maita, N. / Hosokawa, K. / Ueta, S.
History
DepositionOct 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water2,540141
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6440 Å2
Unit cell
Length a, b, c (Å)30.490, 58.040, 67.330
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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 / Fragment: UNP residues 19-148
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O

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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: 2.08 Å3/Da / Density % sol: 40.82 %
Crystal growTemperature: 298 K / Method: batch mode / Details: No precipitants, extensive concentration

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.655→43.961 Å / Num. obs: 14526 / % possible obs: 97.8 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Net I/σ(I): 25.4
Reflection shellResolution: 1.66→1.68 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.235 / Mean I/σ(I) obs: 6.7 / Rpim(I) all: 0.103 / % possible all: 82.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0171refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.66→43.96 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.538 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 755 5.2 %RANDOM
Rwork0.17276 ---
obs0.17484 13691 97.25 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.929 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å2-0 Å2
2---0.44 Å20 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.66→43.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 141 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191025
X-RAY DIFFRACTIONr_bond_other_d0.0030.02904
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.9031389
X-RAY DIFFRACTIONr_angle_other_deg1.11832085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5045128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.962350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.78215166
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7411511
X-RAY DIFFRACTIONr_chiral_restr0.1170.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021172
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02235
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5410.673515
X-RAY DIFFRACTIONr_mcbond_other0.5380.67514
X-RAY DIFFRACTIONr_mcangle_it0.9531.006642
X-RAY DIFFRACTIONr_mcangle_other0.9541.008643
X-RAY DIFFRACTIONr_scbond_it0.6490.76510
X-RAY DIFFRACTIONr_scbond_other0.6480.76510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.1111.108747
X-RAY DIFFRACTIONr_long_range_B_refined5.6889.7341254
X-RAY DIFFRACTIONr_long_range_B_other5.2118.4531219
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.655→1.698 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 47 -
Rwork0.168 850 -
obs--82.75 %

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