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- PDB-4h91: Radiation damage study of lysozyme - 0.35 MGy -

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Basic information

Entry
Database: PDB / ID: 4h91
TitleRadiation damage study of lysozyme - 0.35 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 1.3Sep 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

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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
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.760, 78.760, 36.860
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-375-

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.: 98 / 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: 38.32 %
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
ReflectionRedundancy: 4.5 % / Av σ(I) over netI: 44.08 / Number: 163577 / Rmerge(I) obs: 0.032 / Χ2: 1.15 / D res high: 1.2 Å / D res low: 50 Å / Num. obs: 36589 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.265092.910.0180.9034.4
2.593.2697.710.020.9594.6
2.262.5998.710.0250.9644.6
2.052.2699.310.0311.1884.6
1.92.0598.810.041.1894.5
1.791.999.710.0471.2084.6
1.71.7999.810.0481.1764.5
1.631.799.810.0531.1394.5
1.571.6399.910.061.24.5
1.511.5799.910.0771.2954.5
1.461.5110010.0881.2864.5
1.421.4610010.1011.2534.5
1.391.4210010.1211.2184.5
1.351.3910010.1361.1764.4
1.321.3510010.1531.1944.4
1.291.3210010.1781.1684.4
1.271.2910010.1971.1674.4
1.241.2710010.2361.1334.4
1.221.2410010.2521.1214.4
1.21.2210010.281.0884.3
ReflectionResolution: 1.2→50 Å / Num. all: 36825 / Num. obs: 36589 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5.25 / Redundancy: 4.5 % / Biso Wilson estimate: 11.07 Å2 / Rmerge(I) obs: 0.032 / Rsym value: 0.03 / Χ2: 1.151 / Net I/σ(I): 44.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.224.30.2817991.0881100
1.22-1.244.40.25218041.1211100
1.24-1.274.40.23618311.1331100
1.27-1.294.40.19717911.1671100
1.29-1.324.40.17818231.1681100
1.32-1.354.40.15318061.1941100
1.35-1.394.40.13618201.1761100
1.39-1.424.50.12118191.2181100
1.42-1.464.50.10118191.2531100
1.46-1.514.50.08818111.2861100
1.51-1.574.50.07718361.295199.9
1.57-1.634.50.0618271.2199.9
1.63-1.74.50.05318241.139199.8
1.7-1.794.50.04818321.176199.8
1.79-1.94.60.04718381.208199.7
1.9-2.054.50.0418491.189198.8
2.05-2.264.60.03118451.188199.3
2.26-2.594.60.02518480.964198.7
2.59-3.264.60.0218700.959197.7
3.26-504.40.01818970.903192.9

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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
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6LYZ

6lyz


Resolution: 1.2002→26.911 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8761 / SU ML: 0.3 / σ(F): 1.35 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1994 1834 5.02 %random
Rwork0.1922 ---
all0.198 36825 --
obs0.1925 36554 99.34 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.421 Å2 / ksol: 0.465 e/Å3
Displacement parametersBiso max: 45.71 Å2 / Biso mean: 13.2377 Å2 / Biso min: 6.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.3993 Å20 Å2-0 Å2
2--0.3993 Å20 Å2
3----0.7986 Å2
Refine analyzeLuzzati coordinate error obs: 0.138 Å / Luzzati sigma a obs: 0.044 Å
Refinement stepCycle: LAST / Resolution: 1.2002→26.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 7 98 1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061061
X-RAY DIFFRACTIONf_angle_d1.1021431
X-RAY DIFFRACTIONf_chiral_restr0.084147
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d12.697384
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 (%)
1.2002-1.23270.27071470.246526392786100
1.2327-1.2690.25771300.230926482778100
1.269-1.30990.22831290.219926542783100
1.3099-1.35670.27651350.216826372772100
1.3567-1.4110.21251450.210526492794100
1.411-1.47530.21371550.188126672822100
1.4753-1.5530.22521410.186226562797100
1.553-1.65030.21351220.174926772799100
1.6503-1.77770.18141300.183126942824100
1.7777-1.95660.16221400.18212671281199
1.9566-2.23960.18871570.18222680283799
2.2396-2.82110.1971540.18832699285398
2.8211-26.91750.18971490.19312749289895

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