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- PDB-4h9i: Radiation damage study of lysozyme - 1.05 MGy -

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Basic information

Entry
Database: PDB / ID: 4h9i
TitleRadiation damage study of lysozyme - 1.05 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: 1.2002 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
Revision 1.5Oct 9, 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
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.774, 78.774, 36.870
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-343-

HOH

21A-376-

HOH

31A-379-

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


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.: 107 / 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: 2 Å3/Da / Density % sol: 38.36 %
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: 36843 / Num. obs: 36619 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 4.7 / Redundancy: 4.5 % / Biso Wilson estimate: 11.32 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.03 / Χ2: 1.139 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.224.30.31618041.1261100
1.22-1.244.40.27718081.1121100
1.24-1.274.40.26218201.1211100
1.27-1.294.40.21418031.1451100
1.29-1.324.40.19418271.1381100
1.32-1.354.40.16717981.1731100
1.35-1.394.40.14818281.1721100
1.39-1.424.50.12818181.1661100
1.42-1.464.50.10818161.2281100
1.46-1.514.50.09318111.2221100
1.51-1.574.50.0818381.191199.9
1.57-1.634.50.06518271.208199.9
1.63-1.74.50.05418241.142199.8
1.7-1.794.50.04918361.135199.8
1.79-1.94.60.04818401.139199.7
1.9-2.054.50.0418541.148199
2.05-2.264.60.03118491.006199.4
2.26-2.594.60.02518471.137198.7
2.59-3.264.60.02118671.057197.5
3.26-504.40.01819041.016193.1

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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: 1.2002→26.917 Å / Occupancy max: 1 / Occupancy min: 0.43 / FOM work R set: 0.8716 / SU ML: 0.24 / σ(F): 1.35 / Phase error: 19.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1829 5 %random
Rwork0.1912 ---
all0.197 36843 --
obs0.1918 36582 99.35 %-
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.242 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso max: 34.5 Å2 / Biso mean: 13.5568 Å2 / Biso min: 6.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.4115 Å2-0 Å2-0 Å2
2--0.4115 Å20 Å2
3----0.823 Å2
Refine analyzeLuzzati coordinate error obs: 0.139 Å / Luzzati sigma a obs: 0.044 Å
Refinement stepCycle: LAST / Resolution: 1.2002→26.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 107 1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071061
X-RAY DIFFRACTIONf_angle_d1.1361431
X-RAY DIFFRACTIONf_chiral_restr0.086147
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d12.585384
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 (%)
1.2002-1.23270.24981360.239526492785100
1.2327-1.26890.20251500.224526372787100
1.2689-1.30990.2221200.207826612781100
1.3099-1.35670.26211390.215326372776100
1.3567-1.4110.22781050.208926912796100
1.411-1.47520.20111290.190826922821100
1.4752-1.5530.22381590.188426402799100
1.553-1.65030.20111560.177626412797100
1.6503-1.77770.22891580.185226692827100
1.7777-1.95660.20731200.18162700282099
1.9566-2.23960.18951590.18162680283999
2.2396-2.82110.19931490.18872705285498
2.8211-26.92360.18771490.19082751290095

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