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- PDB-1b0d: Structural effects of monovalent anions on polymorphic lysozyme c... -

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Basic information

Entry
Database: PDB / ID: 1b0d
TitleStructural effects of monovalent anions on polymorphic lysozyme crystals
ComponentsLYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL
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
PARA-TOLUENE SULFONATE / Lysozyme C
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.84 Å
AuthorsVaney, M.C. / Broutin, I. / Retailleau, P. / Lafont, S. / Hamiaux, C. / Prange, T. / Ries-Kautt, M. / Ducruix, A.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structural effects of monovalent anions on polymorphic lysozyme crystals.
Authors: Vaney, M.C. / Broutin, I. / Retailleau, P. / Douangamath, A. / Lafont, S. / Hamiaux, C. / Prange, T. / Ducruix, A. / Ries-Kautt, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Refinement of Triclinic Hen Egg-White Lysozyme at Atomic Resolution
Authors: Walsh, M.A. / Schneider, T.R. / Sieker, L.C. / Dauter, Z. / Lamzin, V.S. / Wilson, K.S.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structures of Monoclinic Lysozyme Iodide at 1.6 Ang. and of Triclinic Lysozyme Nitrate at 1.1 Ang
Authors: Steinrauf, L.K.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Locations of Bromide Ions in Tetragonal Lysozyme Crystals
Authors: Lim, K. / Nadarajah, A. / Forsythe, E.L. / Pusey, M.L.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: High-Resolution Structure (1.33 Ang.) Of a Hewl Lysozyme Tetragonal Crystal Grown in the Apcf Apparatus. Data and Structural Comparison with a Crystal Grown Under Microgravity from Spachab-01 Mission
Authors: Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducruix, A.
History
DepositionNov 7, 1998Deposition site: PDBE / Processing site: NDB
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5032
Polymers14,3311
Non-polymers1721
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.060, 79.060, 37.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-150-

HOH

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Components

#1: Protein LYSOZYME / / HEN (GALLUS GALLUS) EGG-WHITE LYSOZYME / MUCOPEPTIDE / N-ACETYLMURAMYL HYDROLASE


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: CYTOPLASM (WHITE) / Tissue: EGG WHITE / References: UniProt: P00698, lysozyme
#2: Chemical ChemComp-TSU / PARA-TOLUENE SULFONATE / P-Toluenesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.07 Å3/Da / Density % sol: 40.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: THE CRYSTAL WAS OBTAINED IN PRESENCE OF NAPTS WITH A FINAL PROTEIN CONCENTRATION OF 40.5 MG/ML IN HANGING DROPS USING VAPOR DIFFUSION METHOD. THE EQUILIBRATION AT 291K WAS DONE AGAINST A ...Details: THE CRYSTAL WAS OBTAINED IN PRESENCE OF NAPTS WITH A FINAL PROTEIN CONCENTRATION OF 40.5 MG/ML IN HANGING DROPS USING VAPOR DIFFUSION METHOD. THE EQUILIBRATION AT 291K WAS DONE AGAINST A RESERVOIR SOLUTION CONTAINING 90 MM NAPTS, 50 MM SODIUM ACETATE ADJUSTED AT PH 4.5., vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
140.4 mg/mldeionized lysozyme1drop
250 mM1dropNaOAc
390 mMNapTS1reservoir
450 mM1reservoirNaOAc

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 1, 1994
RadiationProtocol: MONOCHROMATIC / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→13.5 Å / Num. obs: 10462 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 21.4 Å2 / Rsym value: 0.049 / Net I/σ(I): 10.5
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.135 / % possible all: 85.8
Reflection
*PLUS
Num. obs: 10484 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
% possible obs: 85.8 % / Rmerge(I) obs: 0.135

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
CCP4model building
X-PLOR3.1refinement
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 1.84→14 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG 61, ARG 73, ASN 77, LYS 97, ASP 101, ASN 103, GLN 121 AND ARG 125 HAVE A POORLY DEFINED DENSITY. THESE ATOMS WERE BUILT USING STEREOCHEMICAL ...Details: SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG 61, ARG 73, ASN 77, LYS 97, ASP 101, ASN 103, GLN 121 AND ARG 125 HAVE A POORLY DEFINED DENSITY. THESE ATOMS WERE BUILT USING STEREOCHEMICAL CONSTRAINTS AND KEPT IN THE COORDINATE FILE.
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1082 10 %RANDOM
Rwork0.202 ---
obs-10461 96.1 %-
Displacement parametersBiso mean: 18.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.84→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 11 86 1098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.33
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.22
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.15
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.521.5
X-RAY DIFFRACTIONx_mcangle_it2.392
X-RAY DIFFRACTIONx_scbond_it2.942
X-RAY DIFFRACTIONx_scangle_it4.722.5
LS refinement shellResolution: 1.84→1.92 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 104 7.71 %
Rwork0.332 1067 -
obs--79.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PRTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
X-RAY DIFFRACTION3PARAMETER.PTSTOPOLOGY.PTS
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.13

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