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- PDB-4h93: Radiation damage study of lysozyme - 0.49 MGy -

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Basic information

Entry
Database: PDB / ID: 4h93
TitleRadiation damage study of lysozyme - 0.49 MGy
ComponentsLysozyme C
KeywordsHYDROLASE
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
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2003 Å
AuthorsSutton, K.A. / Snell, E.H.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Insights into the mechanism of X-ray-induced disulfide-bond cleavage in lysozyme crystals based on EPR, optical absorption and X-ray diffraction studies.
Authors: Sutton, K.A. / Black, P.J. / Mercer, K.R. / Garman, E.F. / Owen, R.L. / Snell, E.H. / Bernhard, W.A.
History
DepositionSep 24, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Database references
Revision 1.2Jan 1, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5005
Polymers14,3311
Non-polymers1684
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.762, 78.762, 36.863
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-349-

HOH

21A-376-

HOH

31A-411-

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: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 7.5% sodium chloride, 100 mM sodium acetate pH 4.8, 25% ethylene glycol, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 12, 2011 / Details: mirrors
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. all: 36827 / Num. obs: 36593 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5 / Redundancy: 4.5 % / Biso Wilson estimate: 11.12 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.03 / Χ2: 1.139 / Net I/σ(I): 15.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.224.30.29218001.0961100
1.22-1.244.40.25918021.1141100
1.24-1.274.40.24618321.1491100
1.27-1.294.40.20517901.1611100
1.29-1.324.40.1818251.145199.9
1.32-1.354.40.1618011.1841100
1.35-1.394.40.14118221.1831100
1.39-1.424.50.12218211.181100
1.42-1.464.50.10118181.1891100
1.46-1.514.50.08918101.2271100
1.51-1.574.50.07918361.265199.9
1.57-1.634.50.06218271.165199.9
1.63-1.74.50.05418261.165199.8
1.7-1.794.50.04918301.173199.8
1.79-1.94.60.04718381.129199.7
1.9-2.054.50.0418501.149198.9
2.05-2.264.60.03118461.048199.4
2.26-2.594.60.02518481.023198.7
2.59-3.264.60.0218691.034197.6
3.26-504.40.01819021.014193.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.7.2_862refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6LYZ

6lyz


Resolution: 1.2003→26.912 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8752 / SU ML: 0.28 / σ(F): 1.33 / Phase error: 19.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 1833 5.01 %random
Rwork0.1905 ---
all0.197 36827 --
obs0.1911 36556 99.34 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.235 Å2 / ksol: 0.469 e/Å3
Displacement parametersBiso max: 40.03 Å2 / Biso mean: 13.4394 Å2 / Biso min: 6.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.3968 Å20 Å2-0 Å2
2--0.3968 Å20 Å2
3----0.7936 Å2
Refine analyzeLuzzati coordinate error obs: 0.138 Å / Luzzati sigma a obs: 0.044 Å
Refinement stepCycle: LAST / Resolution: 1.2003→26.912 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 111 1119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071061
X-RAY DIFFRACTIONf_angle_d1.1091431
X-RAY DIFFRACTIONf_chiral_restr0.084147
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d12.39384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2003-1.23270.28891350.245826482783100
1.2327-1.2690.23981430.229426362779100
1.269-1.30990.21581340.216626472781100
1.3099-1.35680.23741210.216826532774100
1.3568-1.41110.22781370.209526562793100
1.4111-1.47530.21441590.188626632822100
1.4753-1.55310.21011470.186426512798100
1.5531-1.65040.16491270.175226712798100
1.6504-1.77780.19171280.181826972825100
1.7778-1.95660.17611420.18012670281299
1.9566-2.23960.19021570.18042680283799
2.2396-2.82120.19791540.18652699285398
2.8212-26.9190.20481490.19032752290195

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