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- PDB-7br5: Lysozyme-sugar complex in H2O -

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Basic information

Entry
Database: PDB / ID: 7br5
TitleLysozyme-sugar complex in H2O
ComponentsLysozyme C
KeywordsHYDROLASE / Sugar complex
Function / homology
Function and homology information


Lactose synthesis / 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 ...Lactose synthesis / 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
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-like domain superfamily
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsTanaka, I. / Chatake, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H05436 Japan
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Recent structural insights into the mechanism of lysozyme hydrolysis.
Authors: Tanaka, I. / Nishinomiya, R. / Goto, R. / Shimazaki, S. / Chatake, T.
History
DepositionMar 26, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3277
Polymers14,3311
Non-polymers9966
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-12 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.309, 77.309, 38.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

21A-354-

HOH

31A-402-

HOH

41A-450-

HOH

51A-477-

HOH

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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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 1.99 Å3/Da / Density % sol: 38.26 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 4.5
Details: 40mg/mL lysozyme containing 2.1mg/mL (GlcNAc)4, 0.7M NaCl in a buffer of 50mM sodium-acetate (pH4.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→16.833 Å / Num. obs: 61904 / % possible obs: 98.47 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 72.2
Reflection shellResolution: 1→1.02 Å / Rmerge(I) obs: 0.894 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 3096 / CC1/2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4wld

4wld


Resolution: 1→16.833 Å / SU ML: 0.09 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 13.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1669 1998 3.23 %
Rwork0.1392 --
obs0.1401 61904 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→16.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 62 193 1256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071179
X-RAY DIFFRACTIONf_angle_d1.11606
X-RAY DIFFRACTIONf_dihedral_angle_d11.859444
X-RAY DIFFRACTIONf_chiral_restr0.049177
X-RAY DIFFRACTIONf_plane_restr0.004210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0002-1.02520.25031430.21674279X-RAY DIFFRACTION100
1.0252-1.05290.18721420.16634276X-RAY DIFFRACTION100
1.0529-1.08390.1751430.14584266X-RAY DIFFRACTION100
1.0839-1.11890.14171440.12184306X-RAY DIFFRACTION100
1.1189-1.15890.14681420.11744307X-RAY DIFFRACTION100
1.1589-1.20530.13111430.11554278X-RAY DIFFRACTION100
1.2053-1.26010.11741440.1094308X-RAY DIFFRACTION100
1.2601-1.32650.13921440.1094321X-RAY DIFFRACTION100
1.3265-1.40960.13411440.11274324X-RAY DIFFRACTION100
1.4096-1.51840.13591440.11364339X-RAY DIFFRACTION100
1.5184-1.6710.13751460.11674361X-RAY DIFFRACTION100
1.671-1.91250.13771460.13074371X-RAY DIFFRACTION100
1.9125-2.40850.16511480.14114423X-RAY DIFFRACTION100
2.4085-16.8330.22011250.17093747X-RAY DIFFRACTION81

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