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- PDB-1hsx: LYSOZYME GROWN AT BASIC PH AND ITS LOW HUMIDITY VARIANT -

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Basic information

Entry
Database: PDB / ID: 1hsx
TitleLYSOZYME GROWN AT BASIC PH AND ITS LOW HUMIDITY VARIANT
ComponentsLYSOZYME
KeywordsHYDROLASE / GLYCOSIDASE / ENZYME-ORTHORHOMBIC FORM
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: 1.9 Å
AuthorsSukumar, N. / Biswal, B.K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structures of orthorhombic lysozyme grown at basic pH and its low-humidity variant.
Authors: Sukumar, N. / Biswal, B.K. / Vijayan, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Protein Hydration and Water Structure: X-Ray Analysis of a Closely Packed Protein Crystal with Very Low Solvent Content
Authors: Madhusudan / Kodandapani, R. / Vijayan, M.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Refinement of Triclinic Lysozyme. II. The Method of Stereochemically Restrained Least-Squares
Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H.
#3: Journal: J.Biol.Chem. / Year: 1990
Title: Crystal Structure of Low Humidity Tetragonal Lysozyme at 2.1-A Resolution. Variability in Hydration Shell and its Structural Consequences
Authors: Kodandapani, R. / Suresh, C.G. / Vijayan, M.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1982
Title: The Structures of the Monoclinic and Orthorhombic Forms of Hen Egg-White Lysozyme at 6 Angstroms Resolution
Authors: Artymiuk, P.J. / Blake, C.C.F. / Rice, D.W. / Wilson, K.S.
History
DepositionJun 4, 1998Processing site: BNL
Revision 1.0Aug 12, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 1.4Nov 20, 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


Theoretical massNumber of molelcules
Total (without water)14,3311
Polymers14,3311
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.487, 59.583, 68.659
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


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


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.18 Å3/Da / Density % sol: 43 %
Crystal growpH: 9.6 / Details: pH 9.6
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
Method: unknown / pH: 9.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13 %(w/v)protein11
22 %(w/v)11NaClpH9.3

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorDetector: IMAGE PLATE / Date: Jun 3, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 10287 / % possible obs: 99.3 % / Redundancy: 7.08 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.0989 / Net I/σ(I): 26.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 4.8
Reflection
*PLUS
Num. measured all: 72266

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Processing

Software
NameVersionClassification
XDSdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE TETRAGONAL FORM

Resolution: 1.9→10 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.267 391 4.9 %RANDOM
Rwork0.19 ---
obs0.19 8033 78.2 %-
Displacement parametersBiso mean: 23.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1001 0 0 154 1155
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
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_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.891.5
X-RAY DIFFRACTIONx_mcangle_it2.872
X-RAY DIFFRACTIONx_scbond_it3.392
X-RAY DIFFRACTIONx_scangle_it5.032.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.054 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 43 4.7 %
Rwork0.33 875 -
obs--54.8 %
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.62
LS refinement shell
*PLUS
Rfactor Rwork: 0.33

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