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- PDB-4h90: Radiation damage study of lysozyme - 0.28 MGy -

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Basic information

Entry
Database: PDB / ID: 4h90
TitleRadiation damage study of lysozyme - 0.28 MGy
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 / molecular replacement / Resolution: 1.1999 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 1.3Sep 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.758, 78.758, 36.858
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-360-

HOH

21A-382-

HOH

31A-419-

HOH

Detailsbiological unit is the same as asym.

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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


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


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


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 38.32 %
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: 1.1999→50 Å / Num. all: 36830 / Num. obs: 36583 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5.25 / Redundancy: 4.5 % / Biso Wilson estimate: 11.04 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.03 / Net I/σ(I): 45.74
Reflection shellResolution: 1.1999→1.22 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.28 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
PHENIX1.7.2_862refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6LYZ

6lyz


Resolution: 1.1999→26.91 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.878 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 18.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1834 5.01 %random
Rwork0.1893 ---
all0.196 36830 --
obs0.1902 36583 99.34 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.125 Å2 / ksol: 0.463 e/Å3
Displacement parametersBiso max: 41.7 Å2 / Biso mean: 13.4616 Å2 / Biso min: 6.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.4002 Å20 Å2-0 Å2
2--0.4002 Å20 Å2
3----0.8003 Å2
Refine analyzeLuzzati coordinate error obs: 0.137 Å / Luzzati sigma a obs: 0.043 Å
Refinement stepCycle: LAST / Resolution: 1.1999→26.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 119 1127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061061
X-RAY DIFFRACTIONf_angle_d1.0851431
X-RAY DIFFRACTIONf_chiral_restr0.083147
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d12.617384
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 (%)
1.1999-1.23230.2681210.238926632784100
1.2323-1.26860.2231460.227126452791100
1.2686-1.30950.22851330.215826472780100
1.3095-1.35630.23651430.219726342777100
1.3563-1.41060.26431370.205826562793100
1.4106-1.47480.17841550.18626662821100
1.4748-1.55250.19781370.183926612798100
1.5525-1.64980.19821280.172826772805100
1.6498-1.77720.19981420.180226832825100
1.7772-1.9560.17961370.178926852822100
1.956-2.23890.22921530.18042684283799
2.2389-2.82030.21031560.18772698285498
2.8203-26.91640.18891460.18812754290095

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