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- PDB-1bvx: THE 1.8 A STRUCTURE OF GEL GROWN TETRAGONAL HEN EGG WHITE LYSOZYME -

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Basic information

Entry
Database: PDB / ID: 1bvx
TitleTHE 1.8 A STRUCTURE OF GEL GROWN TETRAGONAL HEN EGG WHITE LYSOZYME
ComponentsPROTEIN (LYSOZYME)
KeywordsHYDROLASE / LYSOZYME
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDong, J. / Boggon, T.J. / Chayen, N.E. / Raftery, J. / Bi, R.C. / Helliwell, J.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Bound-solvent structures for microgravity-, ground control-, gel- and microbatch-grown hen egg-white lysozyme crystals at 1.8 A resolution.
Authors: Dong, J. / Boggon, T.J. / Chayen, N.E. / Raftery, J. / Bi, R.C. / Helliwell, J.R.
History
DepositionSep 18, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 30, 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: PROTEIN (LYSOZYME)


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.203, 79.203, 38.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PROTEIN (LYSOZYME)


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SIGMA / Source: (natural) Gallus gallus (chicken) / Cellular location: EGG WHITE / References: UniProt: P00698, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.08 Å3/Da / Density % sol: 40.9 %
Crystal growMethod: grown in gelled protein solution with agarose / pH: 4.5
Details: HEWL CRYSTALS WERE GROWN IN A GELLED PROTEIN SOLUTION WITH AGAROSE (SIGMA, TYPE VII: OF LOW GELLING TEMPERATURE), 4 % MPD IN ACETATE BUFFER (PH 4.5), THE PRECIPITATING AGENT SOL MPD IN ...Details: HEWL CRYSTALS WERE GROWN IN A GELLED PROTEIN SOLUTION WITH AGAROSE (SIGMA, TYPE VII: OF LOW GELLING TEMPERATURE), 4 % MPD IN ACETATE BUFFER (PH 4.5), THE PRECIPITATING AGENT SOL MPD IN BUFFER. THE GLASS TUBE USED WAS 6 CM TALL WITH AN IN CRYSTALS OF TYPICAL DIMENSIONS $SIM$0.7 $TIMES$ 0.6 $TIM, grown in gelled protein solution with agarose
Crystal grow
*PLUS
Method: liquid-gel diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein11
20.2 %agarose11
34 %110.68MNaCl
44 %MPD11
515 %122.57MNaCl
615 %MPD12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE
RadiationMonochromator: CARBON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→99 Å / Num. obs: 12433 / % possible obs: 89.6 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.068 / Rsym value: 0.073 / Net I/σ(I): 21.6
Reflection
*PLUS
Num. measured all: 68445
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 1.74 Å / % possible obs: 51.8 % / Rmerge(I) obs: 0.232

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 193L

193l


Resolution: 1.8→20 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 -5 %RANDOM
Rwork0.182 ---
obs0.182 11073 94.8 %-
Displacement parametersBiso mean: 21.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 95 1096
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
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_deg1.616
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.19
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 21.8 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.19
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.21
LS refinement shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.88 Å / Rfactor Rfree: 0.302 / Rfactor obs: 0.307

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