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- PDB-1bhz: LOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF HEN EGG WHITE LYSO... -

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Basic information

Entry
Database: PDB / ID: 1bhz
TitleLOW TEMPERATURE MIDDLE RESOLUTION STRUCTURE OF HEN EGG WHITE LYSOZYME FROM MASC DATA
ComponentsLYSOZYME
KeywordsHYDROLASE / O-GLYCOSYL / MASC / MULTIWAVELENGTH ANOMALOUS SOLVENT CONTRAST
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, RIGID BODY REFINEMENT / Resolution: 3.9 Å
AuthorsRamin, M. / Shepard, W. / Fourme, R. / Kahn, R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Multiwavelength anomalous solvent contrast (MASC): derivation of envelope structure-factor amplitudes and comparison with model values.
Authors: Ramin, M. / Shepard, W. / Fourme, R. / Kahn, R.
#1: Journal: Nature / Year: 1965
Title: Structure of Hen Egg-White Lysozyme. A Three-Dimensional Fourier Synthesis at 2 Angstrom Resolution
Authors: Blake, C.C. / Koenig, D.F. / Mair, G.A. / North, A.C. / Phillips, D.C. / Sarma, V.R.
History
DepositionJun 10, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.680, 78.680, 37.050
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 LYSOZYME


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG / Cellular location: CYTOPLASM (WHITE) / References: UniProt: P00698, lysozyme
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: 1.9 Å3/Da / Density % sol: 30.3 %
Crystal growDetails: PROTEIN WAS CRYSTALLIZED FROM SODIUM CHLORIDE SOLUTIONS

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Data collection

DiffractionMean temperature: 124 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW21B / Wavelength: 1.39
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.39 Å / Relative weight: 1
ReflectionResolution: 3.91→33.5 Å / Num. obs: 1092 / % possible obs: 84.7 % / Observed criterion σ(I): 3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 18.3
Reflection shellResolution: 3.91→4 Å / Redundancy: 2 % / Rmerge(I) obs: 0.028 / Mean I/σ(I) obs: 46.7 / Rsym value: 0.028 / % possible all: 78
Reflection
*PLUS
Num. measured all: 10257

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
Agrovata(CCP4)data reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, RIGID BODY REFINEMENT
Starting model: 1LSE

1lse


Resolution: 3.9→8 Å / Cross valid method: THROUGHOUT
Rfactor% reflectionSelection details
Rfree0.308 10 %RANDOM
Rwork0.315 --
obs0.315 --
Refinement stepCycle: LAST / Resolution: 3.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 0 0 1156

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